An investigation of the subtype diversity of clinical isolates of Irish Clostridium difficile ribotypes 027 and 078 by repetitive-extragenic palindromic PCR.

LENUS (Irish Health Repository)

Solomon, K

2011-08-01

A repetitive-extragenic palindromic PCR (rep-PCR) subtyping method (DiversiLab) in conjunction with ribotyping, toxinotyping and antimicrobial-susceptibility testing was used to detect subtypes within Clostridium difficile ribotypes 027 and 078. Clinical isolates of ribotypes 027 (toxinotype III) (n = 30) and 078 (toxinotype V) (n = 23) were provided by health-care facilities across the Republic of Ireland over 2 months in 2006 and 1 month in 2009. Ribotype 027 isolates were significantly more related to each other (9 different subtype profiles) when compared to ribotype 078 isolates (14 different profiles) (P = 0.001; cut-off >90 % similarity). Almost half of ribotype 078 isolates (45.5 %) showed no relationship to each other. The clonality of ribotype 027 isolates suggests effective adaptation to the human niche, whereas the considerable genetic diversity within ribotype 078 isolates suggests that they may have originated from a variety of sources. Subtyping correlated well with antimicrobial susceptibility, in particular clindamycin susceptibility for ribotype 027, but diverse antimicrobial-susceptibility profiles were seen in ribotype 078 isolates, even within a single health-care facility. Between 2006 and 2009, a change in the predominant subtype of ribotype 027 was seen, with the recent clone representing half of all ribotype 027 isolates studied. This strain exhibited 89 % similarity to a rep-PCR profile of the North American NAP-1 strain.

Comparison of seasonal soil microbial process in snow-covered temperate ecosystems of northern China.

Directory of Open Access Journals (Sweden)

Xinyue Zhang

Full Text Available More than half of the earth's terrestrial surface currently experiences seasonal snow cover and soil frost. Winter compositional and functional investigations in soil microbial community are frequently conducted in alpine tundra and boreal forest ecosystems. However, little information on winter microbial biogeochemistry is known from seasonally snow-covered temperate ecosystems. As decomposer microbes may differ in their ability/strategy to efficiently use soil organic carbon (SOC within different phases of the year, understanding seasonal microbial process will increase our knowledge of biogeochemical cycling from the aspect of decomposition rates and corresponding nutrient dynamics. In this study, we measured soil microbial biomass, community composition and potential SOC mineralization rates in winter and summer, from six temperate ecosystems in northern China. Our results showed a clear pattern of increased microbial biomass C to nitrogen (N ratio in most winter soils. Concurrently, a shift in soil microbial community composition occurred with higher fungal to bacterial biomass ratio and gram negative (G- to gram positive (G+ bacterial biomass ratio in winter than in summer. Furthermore, potential SOC mineralization rate was higher in winter than in summer. Our study demonstrated a distinct transition of microbial community structure and function from winter to summer in temperate snow-covered ecosystems. Microbial N immobilization in winter may not be the major contributor for plant growth in the following spring.

Mnemiopsis leidyi Gut Harbors Seasonally Variant and Commensal Microbial Assemblages

Science.gov (United States)

Mariita, R. M.; Hossain, M. J.; Liles, M. R.; Moss, A.

2016-02-01

Studies have shown that with widespread use of antibiotics in human and domestic animal populations, antibiotic resistance becomes increasingly common in the environment. Estuaries provide ideal conditions for acquisition and dissemination of drug resistance genes because they serve as sinks for pollution. This study aimed to identify M. leidyi microbial diversity and richness and their potential to act as vectors for antibiotic resistance determinants (ARDs). M. leidyi, although native to study area are highly invasive. Metagenomic analyses indicate that there are temporal variations of bacterioplankton assemblages in M. leidyi gut. Overall, Proteobacteria and Actinobacteria are the most abundant phyla. Despite the temporal dynamics in the microbial assemblages in M. leidyi gut, they seem to retain Propionibacterium acnes (gut microbiota in some insects) and select proteobacteria across all seasons. The results contradict previous studies that suggest that M. leidyi does not have constant a microbiota, but only seasonally variant microbial assemblages. Here we reveal the presence of M. leidyi gut ARDs in winter and summer, probably because of the ctenophores' positive geotaxis during rough surface conditions. Genes responsible for resistance to fluoroquinolones, multidrug resistance efflux pumps, mercuric reductase, copper homeostasis and blaR1 genes were observed. This is the first study to demonstrate that M. leidyi harbors constant microbiota and provides a baseline for understanding M. leidyi gut microbial and ARDs ecology. It also suggests that M. leidyi bacterial taxonomic and functional dynamics is influenced by season. Funding: Alabama EPSCoR GRSP fellowship, AU-CMB fellowship, NSF EPS-1158862, USDA-Hatch 370225-310100 (AGM, ML).

Analysis of proteomes released from in vitro cultured eight Clostridium difficile PCR ribotypes revealed specific expression in PCR ribotypes 027 and 176 confirming their genetic relatedness and clinical importance at the proteomic level

Czech Academy of Sciences Publication Activity Database

Dresler, J.; Krůtová, M.; Fučíková, A.; Klimentová, J.; Hrůzová, V.; Ďuráčová, M.; Houdková, K.; Salovská, B.; Matějková, J.; Hubálek, Martin; Pajer, P.; Píša, L.; Nyč, O.

2017-01-01

Roč. 9, Aug 14 (2017), č. článku 45. ISSN 1757-4749 Institutional support: RVO:61388963 Keywords : Clostridium difficile * label-free quantification * proteome * PCR ribotype 027 * PCR ribotype 176 Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 2.756, year: 2016 https://gutpathogens.biomedcentral.com/articles/10.1186/s13099-017-0194-9

The responses of microbial temperature relationships to seasonal change and winter warming in a temperate grassland.

Science.gov (United States)

Birgander, Johanna; Olsson, Pål Axel; Rousk, Johannes

2018-01-18

Microorganisms dominate the decomposition of organic matter and their activities are strongly influenced by temperature. As the carbon (C) flux from soil to the atmosphere due to microbial activity is substantial, understanding temperature relationships of microbial processes is critical. It has been shown that microbial temperature relationships in soil correlate with the climate, and microorganisms in field experiments become more warm-tolerant in response to chronic warming. It is also known that microbial temperature relationships reflect the seasons in aquatic ecosystems, but to date this has not been investigated in soil. Although climate change predictions suggest that temperatures will be mostly affected during winter in temperate ecosystems, no assessments exist of the responses of microbial temperature relationships to winter warming. We investigated the responses of the temperature relationships of bacterial growth, fungal growth, and respiration in a temperate grassland to seasonal change, and to 2 years' winter warming. The warming treatments increased winter soil temperatures by 5-6°C, corresponding to 3°C warming of the mean annual temperature. Microbial temperature relationships and temperature sensitivities (Q 10 ) could be accurately established, but did not respond to winter warming or to seasonal temperature change, despite significant shifts in the microbial community structure. The lack of response to winter warming that we demonstrate, and the strong response to chronic warming treatments previously shown, together suggest that it is the peak annual soil temperature that influences the microbial temperature relationships, and that temperatures during colder seasons will have little impact. Thus, mean annual temperatures are poor predictors for microbial temperature relationships. Instead, the intensity of summer heat-spells in temperate systems is likely to shape the microbial temperature relationships that govern the soil-atmosphere C

Genomic relationships of Actinobacillus pleuropneumoniae serotype 2 strains evaluated by ribotyping, sequence analysis of ribosomal intergenic regions, and pulsed-field gel electrophoresis

DEFF Research Database (Denmark)

Fussing, V.

1998-01-01

The aim of the present study was to examine the genomic relationship among 112 Actinobacillus pleuropneumoniae serotype 2 strains obtained throughout Europe and North America. HindIII ribotyping of the strains resulted in five ribotypes of high similarity (87-98%). Sequence analysis of the riboso......The aim of the present study was to examine the genomic relationship among 112 Actinobacillus pleuropneumoniae serotype 2 strains obtained throughout Europe and North America. HindIII ribotyping of the strains resulted in five ribotypes of high similarity (87-98%). Sequence analysis...... of the ribosomal intergenic region of strains representing each ribotype and each country showed no differences. A common ribotype was further characterized by PFGE of 12 strains representing all countries. The resultant five PFGE patterns of European strains showed a similarity of more than 91%, to which the two...

Seasonal Changes in Microbial Community Structure in Freshwater Stream Sediment in a North Carolina River Basin

Directory of Open Access Journals (Sweden)

John P. Bucci

2014-01-01

Full Text Available This study examined seasonal differences in microbial community structure in the sediment of three streams in North Carolina’s Neuse River Basin. Microbes that reside in sediment are at the base of the food chain and have a profound influence on the health of freshwater stream environments. Terminal-Restriction Fragment Length Polymorphism (T-RFLP, molecular fingerprint analysis of 16S rRNA genes was used to examine the diversity of bacterial species in stream sediment. Sediment was sampled in both wet and dry seasons from an agricultural (Bear, mixed urban (Crabtree and forested (Marks Creek, and the microbiota examined. Gamma, Alpha and Beta proteobacteria were prevalent species of microbial taxa represented among all sites. Actinobacteria was the next most prevalent species observed, with greater occurrence in dry compared to the wet season. Discernable clustering was observed of Marks and Bear Creek samples collected during the wetter period (September–April, which corresponded with a period of higher precipitation and cooler surface water temperatures. Although not statistically significant, microbial community structure appeared different between season (ANOSIM, R = 0.60; p < 0.10. Principal components analysis confirmed this pattern and showed that the bacterial groups were separated by wet and dry seasonal periods. These results suggest seasonal differences among the microbial community structure in sediment of freshwater streams and that these communities may respond to changes in precipitation during wetter periods.

Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan

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Satoshi Hiraoka

2017-08-01

Full Text Available The presence of microbes in the atmosphere and their transport over long distances across the Earth's surface was recently shown. Precipitation is likely a major path by which aerial microbes fall to the ground surface, affecting its microbial ecosystems and introducing pathogenic microbes. Understanding microbial communities in precipitation is of multidisciplinary interest from the perspectives of microbial ecology and public health; however, community-wide and seasonal analyses have not been conducted. Here, we carried out 16S rRNA amplicon sequencing of 30 precipitation samples that were aseptically collected over 1 year in the Greater Tokyo Area, Japan. The precipitation microbial communities were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria and were overall consistent with those previously reported in atmospheric aerosols and cloud water. Seasonal variations in composition were observed; specifically, Proteobacteria abundance significantly decreased from summer to winter. Notably, estimated ordinary habitats of precipitation microbes were dominated by animal-associated, soil-related, and marine-related environments, and reasonably consistent with estimated air mass backward trajectories. To our knowledge, this is the first amplicon-sequencing study investigating precipitation microbial communities involving sampling over the duration of a year.

Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile.

Science.gov (United States)

Li, Zhirong; Liu, Xiaolei; Zhao, Jianhong; Xu, Kaiyue; Tian, Tiantian; Yang, Jing; Qiang, Cuixin; Shi, Dongyan; Wei, Honglian; Sun, Suju; Cui, Qingqing; Li, Ruxin; Niu, Yanan; Huang, Bixing

2018-04-01

Clostridium difficile is the causative pathogen for antibiotic-related nosocomial diarrhea. For epidemiological study and identification of virulent clones, a new binary typing method was developed for C. difficile in this study. The usefulness of this newly developed optimized 10-loci binary typing method was compared with two widely used methods ribotyping and multilocus sequence typing (MLST) in 189 C. difficile samples. The binary typing, ribotyping and MLST typed the samples into 53 binary types (BTs), 26 ribotypes (RTs), and 33 MLST sequence types (STs), respectively. The typing ability of the binary method was better than that of either ribotyping or MLST expressed in Simpson Index (SI) at 0.937, 0.892 and 0.859, respectively. The ease of testing, portability and cost-effectiveness of the new binary typing would make it a useful typing alternative for outbreak investigations within healthcare facilities and epidemiological research. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparison of a Commercially Available Repetitive-Element PCR System (DiversiLab) with PCR Ribotyping for Typing of Clostridium difficile Strains ▿

OpenAIRE

Eckert, C.; Van Broeck, J.; Spigaglia, P.; Burghoffer, B.; Delmée, M.; Mastrantonio, P.; Barbut, F.

2011-01-01

This study compared a repetitive-element PCR (rep-PCR) method (DiversiLab system) to PCR ribotyping. The discriminatory power of rep-PCR was 0.997. Among the PCR ribotype 027 isolates tested, different rep types could be distinguished. rep-PCR showed a higher discriminatory power than PCR ribotyping. Nevertheless, this method requires technical skill, and visual interpretation of rep-PCR fingerprint patterns may be difficult.

High morbidity and mortality of Clostridium difficile infection and its associations with ribotype 002 in Hong Kong.

Science.gov (United States)

Wong, Sunny H; Ip, Margaret; Hawkey, Peter M; Lo, Norman; Hardy, Katie; Manzoor, Susan; Hui, Wyman W M; Choi, Kin-Wing; Wong, Rity Y K; Yung, Irene M H; Cheung, Catherine S K; Lam, Kelvin L Y; Kwong, Thomas; Wu, William K K; Ng, Siew C; Wu, Justin C Y; Sung, Joseph J Y; Lee, Nelson

2016-08-01

We aim to study the disease burden, risk factors and severity of Clostridium difficile infection (CDI) in Hong Kong. We conducted a prospective, case-control study in three acute-care hospitals in Hong Kong. Adult inpatients who developed CDI diarrhoea confirmed by PCR (n = 139) were compared with the non-CDI controls (n = 114). Ribotyping of isolates and antimicrobial susceptibility testing were performed. The estimated crude annual incidence of CDI was 23-33/100,000 population, and 133-207/100,000 population among those aged ≥65 years. The mean age of CDI patients was 71.5. Nursing home care, recent hospitalization, antibiotics exposure (adjusted OR 3.0, 95% CI 1.3-7.1) and proton-pump inhibitors use (adjusted OR 2.2, 95% CI 1.2-3.9) were risk factors. Severe CDI occurred in 41.7%. Overall mortality was 16.5% (among severe CDI, 26.5%). The commonest ribotypes were 002 (22.8%), 014 (14.1%), 012 and 046; ribotype 027 was absent. Ribotype 002 was associated with fluoroquinolone resistance and higher mortality (47.6% vs. 12.7%; adjusted HR 2.8, 95% CI 1.1-7.0). Our findings show high morbidity and mortality of CDI in the older adults, and identify ribotype 002 as a possible virulent strain causing serious infections in this cohort. Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Microbial quality of yellow seasoned “pindang” fish treated with turmeric and tamarind

Science.gov (United States)

Handayani, B. R.; Dipokusumo, B.; Werdiningsih, W.; Rahayu, T. I.; Sugita, D. L.

2018-01-01

The objective of this study was to determine the microbial quality of yellow seasoned pindang fish. The fish was treated using combination of turmeric and tamarind at different ratio. This research used Randomized Block Design with 2 (two) factors ie concentration of turmeric (0%, 2%, and 6%) and concentration of tamarind (0%, 3%, and 6%). Each treatment was replicated 3 times to obtain 27 experimental units. The parameters observed were total microbe, total fungi and some pathogenic bacteria. Some microbial data were analyzed using descriptive method, however, the number of S. aureus was analyzed at 5% significance level by using software co-Stat and if there was a real difference then tested further by test Honestly Significant Difference (HSD). The results showed that increasing the use of curcumin and tamarind tended to decrease the total number of microbial from treatment control 5.1 x 105 CFU/gram to fish with fungi products contain pathogenic bacteria E. coli Based on microbial quality, it is recommended that the use of 3-6% of turmeric and 2-4% of tamarind are the best spices combination to produce safe consumption of yellow seasoned pindang fish.

Seasonal and diel variability in dissolved DNA and in microbial biomass and activity in a subtropical estuary

International Nuclear Information System (INIS)

Paul, J.H.; Deflaun, M.F.; Jeffrey, W.H.; David, A.W.

1988-01-01

Dissolved DNA and microbial biomass and activity parameters were measured over a 15-month period at three stations along a salinity gradient in Tampa Bay, Fla. Dissolved DNA showed seasonal variation, with minimal values in December and January and maximal values in summer months (July and August). This pattern of seasonal variation followed that of particulate DNA and water temperature and did not correlate with bacterioplankton (direct counts and [ 3 H] thymidine incorporation) or phytoplankton (chlorophyll α and 14 CO 2 fixation) biomass and activity. Microautotrophic populations showed maxima in the spring and fall, whereas microheterotrophic activity was greatest in late summer (September). Both autotrophic and heterotrophic microbial activity was greatest at the high estuarine (low salinity) station and lowest at the mouth of the bay (high salinity station), irrespective of season. Dissolved DNA carbon and phosphorus constituted 0.11 +/- 0.05% of the dissolved organic carbon and 6.6 +/- 6.5% of the dissolved organic phosphorus, respectively. Strong diel periodicity was noted in dissolved DNA and in microbial activity in Bayboro Harbor during the dry season. A noon maximum in primary productivity was followed by an 8 p.m. maximum in heterotrophic activity and a midnight maximum in dissolved DNA. This diel periodicity was less pronounced in the wet season, when microbial parameters were strongly influenced by episodic inputs of freshwater

Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China

Science.gov (United States)

Xu, Bo; Wang, Jinniu; Wu, Ning; Wu, Yan; Shi, Fusun

2018-01-01

Soil microbial activity varies seasonally in frozen alpine soils during cold seasons and plays a crucial role in available N pool accumulation in soil. The intra- and interannual patterns of microbial and nutrient dynamics reflect the influences of changing weather factors, and thus provide important insights into the biogeochemical cycles and ecological functions of ecosystems. We documented the seasonal and interannual dynamics of soil microbial and available N in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China, between April 2011 and October 2013. Soil was collected in the middle of each month and analyzed for water content, microbial biomass C (MBC) and N (MBN), dissolved organic C and N, and inorganic N. Soil microbial community composition was measured by the dilution-plate method. Fungi and actinomycetes dominated the microbial community during the nongrowing seasons, and the proportion of bacteria increased considerably during the early growing seasons. Trends of consistently increasing MBC and available N pools were observed during the nongrowing seasons. MBC sharply declined during soil thaw and was accompanied by a peak in available N pool. Induced by changes in soil temperatures, significant shifts in the structures and functions of microbial communities were observed during the winter-spring transition and largely contributed to microbial reduction. The divergent seasonal dynamics of different N forms showed a complementary nutrient supply pattern during the growing season. Similarities between the interannual dynamics of microbial biomass and available N pools were observed, and soil temperature and water conditions were the primary environmental factors driving interannual fluctuations. Owing to the changes in climate, seasonal soil microbial activities and nutrient supply patterns are expected to change further, and these changes may have crucial implications for the productivity and biodiversity of alpine ecosystems.

Alternative natural seasoning to improve the microbial stability of low-salt beef patties.

Science.gov (United States)

García-Lomillo, Javier; González-SanJosé, M A Luisa; Del Pino-García, Raquel; Rivero-Pérez, M A Dolores; Muñiz-Rodríguez, Pilar

2017-07-15

The meat industry is seeking new strategies to reduce the sodium content of meat products without shortening their shelf-life. Natural seasonings as salt alternatives are more appreciated than chemical preservatives and also enable the incorporation of interesting nutrients. The present work studies the potential of a new red wine pomace seasoning (RWPS), derived from wine pomace, to inhibit spoilage growth in beef patties with different salt levels (2%, 1.5% and 1%) held in storage at 4°C. The use of RWPS (2% w/w) improved the microbial stability of the patties, delaying total aerobic mesophilic, and lactic acid bacteria growth, especially in samples with low salt levels. Satisfactory results were obtained in modified-atmosphere and air-packaged patties. RWPS also enabled the incorporation of fiber and phenolic compounds, and increased potassium and calcium levels. In summary, RWPS presented an interesting potential as a seasoning in meat products, enabling salt reduction without compromising their microbial stability. Copyright © 2017 Elsevier Ltd. All rights reserved.

Seasonality and vertical structure of microbial communities in an ocean gyre

DEFF Research Database (Denmark)

Treusch, Alexander H; Vergin, Kevin L; Finlay, Liam A

2009-01-01

Vertical, seasonal and geographical patterns in ocean microbial communities have been observed in many studies, but the resolution of community dynamics has been limited by the scope of data sets, which are seldom up to the task of illuminating the highly structured and rhythmic patterns of change...

Seasonal variations of indoor microbial exposures and their relation to temperature, relative humidity, and air exchange rate.

Science.gov (United States)

Frankel, Mika; Bekö, Gabriel; Timm, Michael; Gustavsen, Sine; Hansen, Erik Wind; Madsen, Anne Mette

2012-12-01

Indoor microbial exposure has been related to adverse pulmonary health effects. Exposure assessment is not standardized, and various factors may affect the measured exposure. The aim of this study was to investigate the seasonal variation of selected microbial exposures and their associations with temperature, relative humidity, and air exchange rates in Danish homes. Airborne inhalable dust was sampled in five Danish homes throughout the four seasons of 1 year (indoors, n = 127; outdoors, n = 37). Measurements included culturable fungi and bacteria, endotoxin, N-acetyl-beta-d-glucosaminidase, total inflammatory potential, particles (0.75 to 15 μm), temperature, relative humidity, and air exchange rates. Significant seasonal variation was found for all indoor microbial exposures, excluding endotoxin. Indoor fungi peaked in summer (median, 235 CFU/m(3)) and were lowest in winter (median, 26 CFU/m(3)). Indoor bacteria peaked in spring (median, 2,165 CFU/m(3)) and were lowest in summer (median, 240 CFU/m(3)). Concentrations of fungi were predominately higher outdoors than indoors, whereas bacteria, endotoxin, and inhalable dust concentrations were highest indoors. Bacteria and endotoxin correlated with the mass of inhalable dust and number of particles. Temperature and air exchange rates were positively associated with fungi and N-acetyl-beta-d-glucosaminidase and negatively with bacteria and the total inflammatory potential. Although temperature, relative humidity, and air exchange rates were significantly associated with several indoor microbial exposures, they could not fully explain the observed seasonal variations when tested in a mixed statistical model. In conclusion, the season significantly affects indoor microbial exposures, which are influenced by temperature, relative humidity, and air exchange rates.

Characterization of atypical Aeromonas salmonicida isolates by ribotyping and plasmid profiling

DEFF Research Database (Denmark)

Pedersen, Karl; Dalsgaard, Inger; Larsen, J.L.

1996-01-01

A total of 38 strains of atypical Aeromonas salmonicida, three oxidase-negative but otherwise typical Aer. salmonicida, three typical Aer. salmonicida, and two reference strains, isolated from several countries and fish species were examined with respect to rRNA gene restriction patterns (ribotypes...

Diversity of moxifloxacin resistance during a nosocomial outbreak of a predominantly ribotype ARU 027 Clostridium difficile diarrhea.

Science.gov (United States)

Carman, Robert J; Genheimer, Christopher W; Rafii, Fatemeh; Park, Miseon; Hiltonsmith, Megan F; Lyerly, David M

2009-12-01

To characterize the extent and diversity of moxifloxacin resistance among Clostridium difficile isolates recovered during a predominantly Anaerobe Reference Unit (ARU) ribotype 027-associated nosocomial outbreak of antibiotic associated diarrhea we measured the susceptibility of 34 field isolates and 6 laboratory strains of C. difficile to moxifloxacin. We ribotyped the isolates as well as assaying them by PCR for the metabolic gene, gdh, and the virulence genes, tcdA, tcdB, tcdC, cdtA and cdtB. All the laboratory isolates, including the historical ARU 027 isolate Cd196, were susceptible to moxifloxacin (or=16 microg/mL (high resistance). We sequenced the quinolone resistance determining regions of gyrA (position 71-460) and gyrB (position 1059-1448) from two susceptible laboratory strains, all five isolates with moderate resistance and two highly resistant isolates. Two highly resistant isolates (Pitt 40, ribotype ARU 027 and Pitt 33, ribotype ARU 001) had the same C245T (Thr(82)Delta Ile) mutation. No other changes were seen. Amplification with primer pairs specific for the C245T mutant gyrA and for the wild type gene respectively confirmed all 16 highly resistant ARU 027 isolates, as well as the highly resistant isolates from other ribotypes, had the C245T mutation and that the mutation was absent from all other isolates. Among the five isolates with moderate resistance we found combinations of mutations within gyrA (T128A, Val(43)Delta Asp and G349T, Ala(117)Delta Ser) and gyrB (G1276A, Arg(426)Delta Asn). The G1396A (Glu(466)Delta Lys) mutation was not associated with increased resistance.

Ribotyping for differentiating Flavobacterium meningosepticum isolates from clinical and environmental sources

DEFF Research Database (Denmark)

Colding, H; Bangsborg, J; Fiehn, N E

1994-01-01

RI), a discriminatory index of 0.95 to 0.97 was found. The value of ribotyping in an epidemiological setting was assessed for three clinical isolates of F. meningosepticum from an outbreak of meningitis and bacteremia in the neonatal intensive care unit, Rigshospitalet, Copenhagen, Denmark. The three clinical isolates...

Defining microbial community composition and seasonal variation in a sewage treatment plant in India using a down-flow hanging sponge reactor.

Science.gov (United States)

Nomoto, Naoki; Hatamoto, Masashi; Hirakata, Yuga; Ali, Muntjeer; Jayaswal, Komal; Iguchi, Akinori; Okubo, Tsutomu; Takahashi, Masanobu; Kubota, Kengo; Tagawa, Tadashi; Uemura, Shigeki; Yamaguchi, Takashi; Harada, Hideki

2018-05-01

The characteristics of the microbial community in a practical-scale down-flow hanging sponge (DHS) reactor, high in organic matter and sulfate ion concentration, and the seasonal variation of the microbial community composition were investigated. Microorganisms related to sulfur oxidation and reduction (2-27%), as well as Leucobacter (7.50%), were abundant in the reactor. Anaerobic bacteria (27-38% in the first layer) were also in abundance and were found to contribute to the removal of organic matter from the sewage in the reactor. By comparing the Simpson index, the abundance-based coverage estimator (ACE) index, and the species composition of the microbial community across seasons (summer/dry, summer/rainy, autumn/dry, and winter/dry), the microbial community was found to change in composition only during the winter season. In addition to the estimation of seasonal variation, the difference in the microbial community composition along the axes of the DHS reactor was investigated for the first time. Although the abundance of each bacterial species differed along both axes of the reactor, the change of the community composition in the reactor was found to be greater along the vertical axis than the horizontal axis of the DHS reactor.

Performance Assessment of Full-Scale Wastewater Treatment Plants Based on Seasonal Variability of Microbial Communities via High-Throughput Sequencing.

Directory of Open Access Journals (Sweden)

Tang Liu

Full Text Available Microbial communities of activated sludge (AS play a key role in the performance of wastewater treatment processes. However, seasonal variability of microbial population in varying AS-based processes has been poorly correlated with operation of full-scale wastewater treatment systems (WWTSs. In this paper, significant seasonal variability of AS microbial communities in eight WWTSs located in the city of Guangzhou were revealed in terms of 16S rRNA-based Miseq sequencing. Furthermore, variation redundancy analysis (RDA demonstrated that the microbial community compositions closely correlated with WWTS operation parameters such as temperature, BOD, NH4+-N and TN. Consequently, support vector regression models which reasonably predicted effluent BOD, SS and TN in WWTSs were established based on microbial community compositions. This work provided an alternative tool for rapid assessment on performance of full-scale wastewater treatment plants.

Ribotyping of strains of Moraxella (Branhamella) catarrhalis cultured from the nasopharynx and middle ear of children with otitis media

DEFF Research Database (Denmark)

Brygge, K; Sørensen, C H; Colding, H

1998-01-01

Moraxella (Branhaomella) catarrhalis is frequently present in the nasopharyngeal microflora of small children, especially during episodes of acute otitis media . By means of ribotyping (restriction endonuclease analysis of chromosomal DNA combined with rRNA probing), we studied the genetic...... heterogeneity of 78 cultures of M. catarrhalis obtained from different localities in the nasopharynx of nine young children with secretory otitis media. Using HindIII and PstI as endonucleases, five different ribotypes were recognized, representing at least five different genotypes of M. catarrhalis....... The distribution of these types was found to be almost identical to the distribution among 16 M. catarrhalis strains cultured from middle ear exudates of 16 children with acute otitis media. Ribotype HAPA was found in two-thirds of all the cultures investigated, and 44% of the children harboured more than one...

Soil Microbial Activity Responses to Fire in a Semi-arid Savannah Ecosystem Pre- and Post-Monsoon Season

Science.gov (United States)

Jimenez, J. R.; Raub, H. D.; Jong, E. L.; Muscarella, C. R.; Smith, W. K.; Gallery, R. E.

2017-12-01

Extracellular enzyme activities (EEA) of soil microorganisms can act as important proxies for nutrient limitation and turnover in soil and provide insight into the biochemical requirements of microbes in terrestrial ecosystems. In semi-arid ecosystems, microbial activity is influenced by topography, disturbances such as fire, and seasonality from monsoon rains. Previous studies from forest ecosystems show that microbial communities shift to similar compositions after severe fires despite different initial conditions. In semi-arid ecosystems with high spatial heterogeniety, we ask does fire lead to patch intensification or patch homogenization and how do monsoon rains influence the successional trajectories of microbial responses? We analyzed microbial activity and soil biogeochemistry throughout the monsoon season in paired burned and unburned sites in the Santa Rita Experimental Range, AZ. Surface soil (5cm) from bare-ground patches, bole, canopy drip line, and nearby grass patches for 5 mesquite trees per site allowed tests of spatiotemporal responses to fire and monsoon rain. Microbial activity was low during the pre-monsoon season and did not differ between the burned and unburned sites. We found greater activity near mesquite trees that reflects soil water and nutrient availability. Fire increased soil alkalinity, though soils near mesquite trees were less affected. Soil water content was significantly higher in the burned sites post-monsoon, potentially reflecting greater hydrophobicity of burned soils. Considering the effects of fire in these semi-arid ecosystems is especially important in the context of the projected changing climate regime in this region. Assessing microbial community recovery pre-, during, and post-monsoon is important for testing predictions about whether successional pathways post-fire lead to recovery or novel trajectories of communities and ecosystem function.

Diversity of Clostridium difficile PCR ribotypes in Europe: results from the European, multicentre, prospective, biannual, point-prevalence study of Clostridium difficile infection in hospitalised patients with diarrhoea (EUCLID), 2012 and 2013.

Science.gov (United States)

Davies, Kerrie A; Ashwin, Helen; Longshaw, Christopher M; Burns, David A; Davis, Georgina L; Wilcox, Mark H

2016-07-21

Clostridium difficile infection (CDI) is the major cause of infective diarrhoea in healthcare environments. As part of the European, multicentre, prospective, biannual, point-prevalence study of Clostridium difficile infection in hospitalised patients with diarrhoea (EUCLID), the largest C. difficile epidemiological study of its type, PCR ribotype distribution of C. difficile isolates in Europe was investigated. PCR ribotyping was performed on 1,196 C. difficile isolates from diarrhoeal samples sent to the European coordinating laboratory in 2012-13 and 2013 (from two sampling days) by 482 participating hospitals from 19 European countries. A total of 125 ribotypes were identified, of which ribotypes 027 (19%, n =222), 001/072 (11%, n = 134) and 014/020 (10%, n = 119) were the most prevalent. Distinct regional patterns of ribotype distribution were noted. Of 596 isolates from patients with toxin-positive stools (CDI cases), ribotype 027 accounted for 22% (32/144) of infections in cases aged from 18 to less than 65 years, but the prevalence decreased in those aged ≥ 65 years (14% (59/412)) and further decreased in those aged ≥ 81 years (9% (18/195)). The prevalence of ribotype 027 and 176, but not other epidemic strains, was inversely proportional to overall ribotype diversity (R(2) = 0.717). This study highlights an increased diversity of C. difficile ribotypes across Europe compared with previous studies, with considerable intercountry variation in ribotype distribution. Continuous surveillance programmes are necessary to monitor the changing epidemiology of C. difficile. This article is copyright of The Authors, 2016.

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study.

Science.gov (United States)

Smith, A Peyton; Marín-Spiotta, Erika; Balser, Teri

2015-09-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land-cover change affects belowground carbon storage and nutrient availability. We measured intra- and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well-replicated, long-term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter- and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land-use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities. © 2015 John Wiley & Sons Ltd.

Seasonal Development of Microbial Activity in Soils of Northern Norway

Institute of Scientific and Technical Information of China (English)

M. B(O)LTER; N. SOETHE; R. HORN; C. UHLIG

2005-01-01

Seasonal development of soil microbial activity and bacterial biomass in sub-polar regions was investigated to determine the impacts of biotic and abiotic factors, such as organic matter content, temperature and moisture. The study was performed during spring thaw from three cultivated meadows and two non-cultivated forest sites near Alta, in northern Norway. Samples from all five sites showed increasing respiration rates directly after the spring thaw with soil respiration activity best related to soil organic matter content. However, distributions of bacterial biomass showed fewer similarities to these two parameters. This could be explained by variations of litter exploitation through the biomass. Microbial activity started immediately after the thaw while root growth had a longer time lag. An influence of root development on soil microbes was proposed for sites where microorganisms and roots had a tight relationship caused by a more intensive root structure. Also a reduction of microbial activity due to soil compaction in the samples from a wheel track could not be observed under laboratory conditions. New methodological approaches of differential staining for live and dead organisms were applied in order to follow changes within the microbial community. Under laboratory conditions freeze and thaw cycles showed a damaging influence on parts of the soil bacteria. Additionally, different patterns for active vs.non-active bacteria were noticeable after freeze-thaw cycles.

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters.

Science.gov (United States)

Oberbeckmann, Sonja; Loeder, Martin G J; Gerdts, Gunnar; Osborn, A Mark

2014-11-01

Plastic pollution is now recognised as a major threat to marine environments and marine biota. Recent research highlights that diverse microbial species are found to colonise plastic surfaces (the plastisphere) within marine waters. Here, we investigate how the structure and diversity of marine plastisphere microbial community vary with respect to season, location and plastic substrate type. We performed a 6-week exposure experiment with polyethylene terephthalate (PET) bottles in the North Sea (UK) as well as sea surface sampling of plastic polymers in Northern European waters. Scanning electron microscopy revealed diverse plastisphere communities comprising prokaryotic and eukaryotic microorganisms. Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. Polymers sampled from the sea surface mainly comprised polyethylene, polystyrene and polypropylene particles. Variation within plastisphere communities on different polymer types was observed, but communities were primarily dominated by Cyanobacteria. This research reveals that the composition of plastisphere microbial communities in marine waters varies with season, geographical location and plastic substrate type. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Dynamics in Microbial Composition and Functionality over a Season in Two Contrasting Estuarine Systems

DEFF Research Database (Denmark)

Traving, Sachia; Bentzon-Tilia, Mikkel; Mantikci, Mustafa

2015-01-01

In aquatic microbial ecology it remains unclear how bacterial community composition and dynamics are coupled to functionality, and whether this putative coupling varies over the season. In this study we address the questions if bacterial community composition can be linked to community function, ...

Climate change in winter versus the growing-season leads to different effects on soil microbial activity in northern hardwood forests

Science.gov (United States)

Sorensen, P. O.; Templer, P. H.; Finzi, A.

2014-12-01

Mean winter air temperatures have risen by approximately 2.5˚ C per decade over the last fifty years in the northeastern U.S., reducing the maximum depth of winter snowpack by approximately 26 cm over this period and the duration of winter snow cover by 3.6 to 4.2 days per decade. Forest soils in this region are projected to experience a greater number of freeze-thaw cycles and lower minimum winter soil temperatures as the depth and duration of winter snow cover declines in the next century. Climate change is likely to result not only in lower soil temperatures during winter, but also higher soil temperatures during the growing-season. We conducted two complementary experiments to determine how colder soils in winter and warmer soils in the growing-season affect microbial activity in hardwood forests at Harvard Forest, MA and Hubbard Brook Experimental Forest, NH. A combination of removing snow via shoveling and buried heating cables were used to induce freeze-thaw events during winter and to warm soils 5˚C above ambient temperatures during the growing-season. Increasing the depth and duration of soil frost via snow-removal resulted in short-term reductions in soil nitrogen (N) production via microbial proteolytic enzyme activity and net N mineralization following snowmelt, prior to tree leaf-out. Declining mass specific rates of carbon (C) and N mineralization associated with five years of snow removal at Hubbard Brook Experimental Forest may be an indication of microbial physiological adaptation to winter climate change. Freeze-thaw cycles during winter reduced microbial extracellular enzyme activity and the temperature sensitivity of microbial C and N mineralization during the growing-season, potentially offsetting nutrient and soil C losses due to soil warming in the growing-season. Our multiple experimental approaches show that winter climate change is likely to contribute to reduced microbial activity in northern hardwood forests.

Subboiling Moist Heat Favors the Selection of Enteric Pathogen Clostridium difficile PCR Ribotype 078 Spores in Food

Directory of Open Access Journals (Sweden)

Alexander Rodriguez-Palacios

2016-01-01

Full Text Available Emerging enteric pathogens could have not only more antibiotic resistance or virulence traits; they could also have increased resistance to heat. We quantified the effects of minimum recommended cooking and higher temperatures, individually on a collection of C. difficile isolates and on the survival probability of a mixture of emerging C. difficile strains. While minimum recommended cooking time/temperature combinations (63–71°C allowed concurrently tested strains to survive, higher subboiling temperatures reproducibly favored the selection of newly emerging C. difficile PCR ribotype 078. Survival ratios for “ribotypes 078” :  “other ribotypes” (n=49 : 45 isolates from the mid-2000s increased from 1 : 1 and 0.7 : 1 at 85°C (for 5 and 10 minutes, resp. to 2.3 : 1 and 3 : 1 with heating at 96°C (for 5 and 10 minutes, resp. indicating an interaction effect between the heating temperature and survival of C. difficile genotypes. In multistrain heating experiments, with PCR ribotypes 027 and 078 from 2004 and reference type strain ATCC 9689 banked in the 1970s, multinomial logistic regression (P<0.01 revealed PCR ribotype 078 was the most resistant to increasing lethal heat treatments. Thermal processes (during cooking or disinfection may contribute to the selection of emergent specific virulent strains of C. difficile. Despite growing understanding of the role of cooking on human evolution, little is known about the role of cooking temperatures on the selection and evolution of enteric pathogens, especially spore-forming bacteria.

Hospital-based Clostridium difficile infection surveillance reveals high proportions of PCR ribotypes 027 and 176 in different areas of Poland, 2011 to 2013.

Science.gov (United States)

Pituch, Hanna; Obuch-Woszczatyński, Piotr; Lachowicz, Dominika; Wultańska, Dorota; Karpiński, Paweł; Młynarczyk, Grażyna; van Dorp, Sofie M; Kuijper, Ed J

2015-01-01

As part of the European Clostridium difficile infections (CDI) surveillance Network (ECDIS-Net), which aims to build capacity for CDI surveillance in Europe, we constructed a new network of hospital-based laboratories in Poland. We performed a survey in 13 randomly selected hospital-laboratories in different sites of the country to determine their annual CDI incidence rates from 2011 to 2013. Information on C. difficile laboratory diagnostic testing and indications for testing was also collected. Moreover, for 2012 and 2013 respectively, participating hospital-laboratories sent all consecutive isolates from CDI patients between February and March to the Anaerobe Laboratory in Warsaw for further molecular characterisation, including the detection of toxin-encoding genes and polymerase chain reaction (PCR)-ribotyping. Within the network, the mean annual hospital CDI incidence rates were 6.1, 8.6 and 9.6 CDI per 10,000 patient-days in 2011, 2012, and 2013 respectively. Six of the 13 laboratories tested specimens only on the request of a physician, five tested samples of antibiotic-associated diarrhoea or samples from patients who developed diarrhoea more than two days after admission (nosocomial diarrhoea), while two tested all submitted diarrhoeal faecal samples. Most laboratories (9/13) used tests to detect glutamate dehydrogenase and toxin A/B either separately or in combination. In the two periods of molecular surveillance, a total of 166 strains were characterised. Of these, 159 were toxigenic and the majority belonged to two PCR-ribotypes: 027 (n=99; 62%) and the closely related ribotype 176 (n=22; 14%). The annual frequency of PCR-ribotype 027 was not significantly different during the surveillance periods (62.9% in 2012; 61.8% in 2013). Our results indicate that CDIs caused by PCR-ribotype 027 predominate in Polish hospitals participating in the surveillance, with the closely related 176 ribotype being the second most common agent of infection.

Shedding of Clostridium difficile PCR ribotype 078 by zoo animals, and report of an unstable metronidazole-resistant isolate from a zebra foal (Equus quagga burchellii).

Science.gov (United States)

Álvarez-Pérez, Sergio; Blanco, José L; Martínez-Nevado, Eva; Peláez, Teresa; Harmanus, Celine; Kuijper, Ed; García, Marta E

2014-03-14

Clostridium difficile is an emerging and potentially zoonotic pathogen, but its prevalence in most animal species, including exhibition animals, is currently unknown. In this study we assessed the prevalence of faecal shedding of C. difficile by zoo animals, and determined the ribotype, toxin profile and antimicrobial susceptibility of recovered isolates. A total of 200 samples from 40 animal species (36.5% of which came from plains zebra, Equus quagga burchellii) were analysed. C. difficile was isolated from 7 samples (3.5% of total), which came from the following animal species: chimpanzee (Pan troglodytes troglodytes), dwarf goat (Capra hircus), and Iberian ibex (Capra pyrenaica hispanica), with one positive sample each; and plains zebra, with 4 positive samples from 3 different individuals. Most recovered isolates (4/7, 57.1%) belonged to the epidemic PCR ribotype 078, produced toxins A and B, and had the genes encoding binary toxin (i.e. A(+)B(+)CDT(+) isolates). The remaining three isolates belonged to PCR ribotypes 039 (A(-)B(-)CDT(-)), 042 (A(+)B(+)CDT(-)) and 110 (A(-)B(+)CDT(-)). Regardless of their ribotype, all isolates displayed high-level resistance to the fluoroquinolones ciprofloxacin, enrofloxacin and levofloxacin. Some isolates were also resistant to meropenem and/or ertapenem. A ribotype 078 isolate recovered from a male zebra foal initially showed in vitro resistance to metronidazole (MIC ≥ 256 μg/ml), but lost that trait after subculturing on non-selective media. We conclude that zoo animals belonging to different species can carry ribotype 078 and other toxigenic strains of C. difficile showing resistance to antimicrobial compounds commonly used in veterinary and/or human medicine. Copyright © 2014 Elsevier B.V. All rights reserved.

Ribotypes and AP-PCR fingerprints of thermophilic campylobacters from marine recreational waters.

Science.gov (United States)

Hernández, J; Fayos, A; Alonso, J L; Owen, R J

1996-02-01

Thirty-two strains of thermophilic campylobacters isolated from marine recreational water and seven reference strains were biotyped and analysed by chromosomal DNA HaeIII ribopatterns and AP-PCR profiles based on a random 10-mer primer (5'-CAA TCG CCG T-3'). The majority of seawater isolates (90%) were Campylobacter coli, and three strains were Camp. jejuni. Southern blot hybridization analysis showed differences between the strains, and in a numerical analysis three main clusters were formed at the 45% similarity level, that corresponded to Camp. jejuni subsp. jejuni, Camp. coli, and a combination of Camp. coli and Camp. jejuni subsp. doylei. AP-PCR profiles also differentiated between the species but were less discriminatory than ribotyping because six strains (17%) could not be typed by this method. Numerical analysis gave four main clusters at the 45% similarity level, corresponding to Camp. jejuni subsp. jejuni, Camp. coli (two clusters) and Camp. lari. The study shows that strains within each species are diverse genomically. Both molecular methods were highly discriminatory, although some strains with identical ribotypes could be distinguished by AP-PCR, and they are valuable new alternatives to traditional typing in epidemiological studies of environmental campylobacters.

Correlation between fecal calprotectin levels, disease severity and the hypervirulent ribotype 027 strain in patients with Clostridium difficile infection.

Science.gov (United States)

Peretz, Avi; Tkhawkho, Linda; Pastukh, Nina; Brodsky, Diana; Halevi, Chen Namimi; Nitzan, Orna

2016-06-22

Clostridium difficile is the most common infectious etiology of nosocomial diarrhea. Fecal calprotectin (fc) is a sensitive marker of intestinal inflammation, found to be associated with enteric bacterial infections and inflammatory bowel disease. We evaluated fc levels using a Chemiluminescent immunoassay method, in hospitalized patients with C. difficile infection (CDI) diagnosed by molecular stool examination and assessed correlation with virulent ribotype 027 strain infection, antibiotic susceptibility by gradient Etest strip performed on C. difficile colonies and clinical and laboratory measures of disease severity. Statistical analysis was performed for correlation of fc levels with clinical and laboratory parameters, disease severity and patient outcomes. Overall 29 patients with CDI were admitted at the Poria medical center in northern Israel, during June 2014-May 2015. Resistance to metronidazole was found in 3 (10.3 %) isolates and to vancomycin in 5 (17.2 %) isolates. Regarding patient outcomes, within 30 days of CDI diagnosis, recurrence of disease occurred in 10 (34.5 %) patients and 2 patients (6.9 %) died. Seven (24.1 %) isolates were C. difficile ribotype 027. Mean fc level was 331.4 μg/g (21-932). Higher fc levels were found in patients with C. difficile ribotype 027 (p clostridium severity score index (p = 0.0633). No correlation was found between fecal calprotectin levels and age, sex, functional status, community versus hospital acquired CDI, antibiotic susceptibility, fever, and creatinine levels. Our study highlights the fact that fc has a potential role as a biomarker of disease severity and binary toxin producing ribotype associated disease.

Effect of storage time on microbial quality of some spices and dried seasonings

International Nuclear Information System (INIS)

Adu-Gyamfi, A.

2006-01-01

The effect of storage time on the microbial quality of some spices and dried seasonings (SOS) (dawadawa, pepper, ginger, shrimp and fish powders) was studied over a 12-month period. Microbial load and profile of irradiated and unirradiated SOS were assessed at 0, 6 and 12-month periods. The range of total variable counts (TVCs) were initially determined at 0.81-4.53 and 4.658.51 log 10 cfu g -1 for irradiated and un irradiated SDS, respectively; those for mould and yeast counts (MYCs) were determined at 0-1.74 and 1.55-3.35 log 10 cfu g -1 , respectively. Generally, TVCs were not significantly affected (P<0.05) by the 6 and 12-month periods, but MYCs were significantly reduced (P<0.05) after the storage periods in some SDS. Microbial profile, mainly dominated by Bacillus spp., Laclobacillus spp., Clostridium spp., Aspergillus spp. and Penicillium spp., was stable after the 6 and 12-month periods for all the SDS. However, the profile was consistently more diverse on dawadawa. pepper and ginger powders. No adverse change in microbial quality of irradiated and unirradiated SDS was observed at the end of the storage periods

Ribotyping on small-sized spirochetes isolated from subgingival plaque

DEFF Research Database (Denmark)

Fiehn, N E; Bangsborg, J M; Colding, H

1995-01-01

distinct bands were observed for the 2:4:2 isolates and the T. denticola strains. For each of the endonucleases used, identical band patterns were always observed for this group of isolates, and these patterns differed persistently from the T. denticola strains. For the 1:2:1 strains, up to 11 distinct...... bands were observed after digestion with HindIII, whereas a maximum of 6 bands were observed when PstI or ClaI was used. By using ClaI, the examined 1:2:1 isolates were separated into 8 groups, whereas PstI and HindIII separated these isolates into 5 groups. The ribotyping showed that the tested 1...

Seasonal variations of the composition of microbial biofilms in sandy tidal flats: Focus of fatty acids, pigments and exopolymers

Science.gov (United States)

Passarelli, Claire; Meziane, Tarik; Thiney, Najet; Boeuf, Dominique; Jesus, Bruno; Ruivo, Mickael; Jeanthon, Christian; Hubas, Cédric

2015-02-01

Biofilms, or microbial mats, are common associations of microorganisms in tidal flats; they generally consist of a large diversity of organisms embedded in a matrix of Extracellular Polymeric Substances (EPS). These molecules are mainly composed of carbohydrates and proteins, but their detailed monomer compositions and seasonal variations are currently unknown. Yet this composition determines the numerous roles of biofilms in these systems. This study investigated the changes in composition of carbohydrates in intertidal microbial mats over a year to decipher seasonal variations in biofilms and in varying hydrodynamic conditions. This work also aimed to assess how these compositions are related to microbial assemblages. In this context, natural biofilms whose development was influenced or not by artificial structures mimicking polychaete tubes were sampled monthly for over a year in intertidal flats of the Chausey archipelago. Biofilms were compared through the analysis of their fatty acid and pigment contents, and the monosaccharide composition of their EPS carbohydrates. Carbohydrates from both colloidal and bound EPS contained mainly glucose and, to a lower extent, galactose and mannose but they showed significant differences in their detailed monosaccharide compositions. These two fractions displayed different seasonal evolution, even if glucose accumulated in both fractions in summer; bound EPS only were affected by artificial biogenic structures. Sediment composition in fatty acids and pigments showed that microbial communities were dominated by diatoms and heterotrophic bacteria. Their relative proportions, as well as those of other groups like cryptophytes, changed between times and treatments. The changes in EPS composition were not fully explained by modifications of microbial assemblages but also depended on the processes taking place in sediments and on environmental conditions. These variations of EPS compositions are likely to alter different

Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats

Directory of Open Access Journals (Sweden)

Mercedes Berlanga

2017-12-01

Full Text Available Microbial mats are complex biofilms in which the major element cycles are represented at a millimeter scale. In this study, community variability within microbial mats from the Camargue wetlands (Rhone Delta, southern France were analyzed over 3 years during two different seasons (spring and autumn and at different layers of the mat (0–2, 2–4, and 4–6 mm. To assess bacterial diversity in the mats, amplicons of the V1–V2 region of the 16S rRNA gene were sequenced. The community’s functionality was characterized using two approaches: (i inferred functionality through 16S rRNA amplicons genes according to PICRUSt, and (ii a shotgun metagenomic analysis. Based on the reads distinguished, microbial communities were dominated by Bacteria (∼94%, followed by Archaea (∼4% and Eukarya (∼1%. The major phyla of Bacteria were Proteobacteria, Bacteroidetes, Spirochaetes, Actinobacteria, Firmicutes, and Cyanobacteria, which together represented 70–80% of the total population detected. The phylum Euryarchaeota represented ∼80% of the Archaea identified. These results showed that the total bacterial diversity from the Camargue microbial mats was not significantly affected by seasonal changes at the studied location; however, there were differences among layers, especially between the 0–2 mm layer and the other two layers. PICRUSt and shotgun metagenomic analyses revealed similar general biological processes in all samples analyzed, by season and depth, indicating that different layers were functionally stable, although some taxa changed during the spring and autumn seasons over the 3 years. Several gene families and pathways were tracked with the oxic-anoxic gradient of the layers. Genes directly involved in photosynthesis (KO, KEGG Orthology were significantly more abundant in the top layer (0–2 mm than in the lower layers (2–4 and 4–6 mm. In the anoxic layers, the presence of ferredoxins likely reflected the variation of redox

Spread and epidemiology of Clostridium difficile polymerase chain reaction ribotype 027/toxinotype III in The Netherlands

NARCIS (Netherlands)

Goorhuis, A.; van der Kooi, T.; Vaessen, N.; Dekker, F. W.; van den Berg, R.; Harmanus, C.; van den Hof, S.; Notermans, D. W.; Kuijper, E. J.

2007-01-01

After reports of emerging outbreaks in Canada and the United States, Clostridium difficile-associated disease (CDAD) due to polymerase chain reaction ribotype 027 was detected in 2 medium-to-large hospitals in The Netherlands in 2005. National surveillance was initiated to investigate the spread and

Composition and function of the microbial community related with the nitrogen cycling on the potato rhizosphere

International Nuclear Information System (INIS)

Florez Zapata, Nathalia; Garcia, Juan Carlos; Del Portillo, Patricia; Restrepo, Silvia; Uribe Velez, Daniel

2013-01-01

In the S. tuberosum group phureja crops, mineral fertilizer and organic amendments are applied to meet the plants nutritional demands, however the effect of such practices on the associated rizospheric microbial communities are still unknown. Nitrogen plays an important role in agricultural production, and a great diversity of microorganisms regulates its transformation in the soil, affecting its availability for the plant. The aim of this study was to assess the structure of microbial communities related with the N cycle of S. tuberosum group phureja rizospheric soil samples, with contrasting physical-chemical properties and fertilization strategy. Few significant differences between the community compositions at the phylum level were found, only Planctomycetes phylum was different between samples of different soil type and fertilization strategy. However, the analysis of nitrogen-associated functional groups made by ribotyping characterization, grouped soils in terms of such variables in a similar way to the physical-chemical properties. Major differences between soil samples were typified by higher percentages of the ribotypes from nitrite oxidation, nitrogen fixation and denitrification on organic amendment soils. Our results suggest that, the dominant rhizosphere microbial composition is very similar between soils, possibly as a result of population's selection mediated by the rhizosphere effect. However, agricultural management practices in addition to edaphic properties of sampled areas appear to affect some functional groups associated with the nitrogen cycling, due to differences found on soil's physicalchemical properties, like the concentration of ammonium that seems to have an effect regulating the distribution and activity of nitrogen related functional groups in the S. tuberosum rhizosphere.

Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil.

Science.gov (United States)

Resende, Juliana Alves; Godon, Jean-Jacques; Bonnafous, Anaïs; Arcuri, Pedro Braga; Silva, Vânia Lúcia; Otenio, Marcelo Henrique; Diniz, Cláudio Galuppo

2016-04-01

Anaerobic digestion is an alternative method for the treatment of animal manure and wastewater. The anaerobic bioconversion of biomass requires a multi-step biological process, including microorganisms with distinct roles. The diversity and composition of microbial structure in pilot-scale anaerobic digestion operating at ambient temperature in Brazil were studied. Influence of the seasonal and temporal patterns on bacterial and archaeal communities were assessed by studying the variations in density, dynamic and diversity and structure. The average daily biogas produced in the summer and winter months was 18.7 and 16 L day(-1), respectively, and there was no difference in the average methane yield. Quantitative PCR analysis revealed that no differences in abundances and dynamics were found for bacterial communities and the total number of Archaea in different seasons. Analysis of bacterial clone libraries revealed a predominance of Firmicutes (54.5 %/summer and 46.7 %/winter) and Bacteroidetes (31.4 %/summer and 44.4 %/winter). Within the Archaea, the phylum Euryarchaeota was predominant in both digesters. Phylogenetic distribution showed changes in percentage between the phyla identified, but no alterations were recorded in the quality and amount of produced methane or community dynamics. The results may suggest that redundancy of microbial groups may have occurred, pointing to a more complex microbial community in the ecosystem related to this ambient temperature system.

Emergence of Clostridium difficile infection due to a new hypervirulent strain, polymerase chain reaction ribotype 078

NARCIS (Netherlands)

Goorhuis, Abraham; Bakker, Dennis; Corver, Jeroen; Debast, Sylvia B.; Harmanus, Celine; Notermans, Daan W.; Bergwerff, Aldert A.; Dekker, Frido W.; Kuijper, Ed J.

2008-01-01

Since 2005, an increase in the prevalence of Clostridium difficile infection (CDI) due to polymerase chain reaction ribotype 078 has been noticed in The Netherlands. This strain has also been identified as the predominant strain in pigs and calves. CDI caused by type 078 was studied in relation to

The Recent Emergence of Clostridium difficile Infection in Romanian Hospitals is Associated with a High Prevalence of Polymerase Chain Reaction Ribotype 027

Directory of Open Access Journals (Sweden)

Gabriel Adrian Popescu

2018-03-01

Full Text Available Aims: To investigate the epidemiology of Clostridium difficile infection in Romanian hospitals. Methods: A survey was conducted at nine hospitals throughout Romania between November 2013 and February 2014. Results: The survey identified 393 patients with Clostridium difficile infection. The median age was 67 years (range: 2-94 years; 56% of patients were aged >65 years. The mean prevalence of Clostridium difficile infection was 5.2 cases per 10.000 patient-days. The highest prevalences were 24.9 and 20 per 10.000 patient-days in hospitals specializing in gastroenterology and infectious diseases, respectively. Clostridium difficile infections were health care-associated in 70.5% patients and community-acquired in 10.2%. The origin was not determined in 19.3%. Clostridium difficile infection was severe in 12.3% of patients, and the in-hospital all-cause mortality was 8.8%. Polymerase chain reaction ribotype 027 had the highest prevalence in all participating hospitals and represented 82.6% of the total ribotyped isolates. The minimum inhibitory concentration of moxifloxacin was >4 μg/mL for 59 of 80 tested isolates (73.8%. Of 59 isolates, 54 were highly resistant to moxifloxacin (minimum inhibitory concentration ≥32 μg/mL, and the majority were polymerase chain reaction ribotype 027 (p<0.0001. Conclusion: The ribotype 027 was the predominant cause of Clostridium difficile infections in Romania. In some specialized hospitals, the prevalence of Clostridium difficile infection was higher than the European mean prevalence, and this demonstrates the need for strict adherence to infection control programs.

Seasonal and spatial variations in microbial activity at various phylogenetic resolutions at a groundwater – surface water interface

DEFF Research Database (Denmark)

Yu, Ran; Smets, Barth F.; Gan, Ping

2014-01-01

analysis. Consistently higher microbial activities with less variation in depth were measured in the AIMC traps than in the ambient sediments. Flood disturbance appeared to control AIMC activity distributions at the gradually elevated GSI. The highest AIMC activities were generally obtained from locations...... closest to the free surface water boundary except during the dry season when microbial activities were similar across the entire GSI. A clone library of AIMC 16S rRNA genes was constructed, and it confirmed the predominant role of the targeted alphaproteobacterial group in AIMC activity and composition...... phylogenetically related to putative IOB, supporting the occurrence and persistence of active microbial iron oxidation across the studied iron-rich GSI ecosystem....

A study of phage- and ribotype patterns of Staphylococcus aureus isolated from bovine mastitis in the Nordic countries

DEFF Research Database (Denmark)

Aarestrup, Frank Møller; Wegener, Henrik Caspar; Jensen, N.E.

1997-01-01

This study was conducted to investigate the geographical distribution of phage and ribotypes of Staphylococcus aureus causing bovine mastitis in the 5 Nordic countries. A total of 403 isolates of S. aureus was isolated from 403 different dairy herds. One hundred five strains were isolated...... of the isolates of ribotype 1 belonged to phage type 29/52. This combined type accounted for 17% of all the 403 isolates. These findings show that a large number of different types of S. aureus can be isolated from cases of bovine mastitis. However, few types predominate within different countries....... These predominating types seem to be specific in each country, however, a single type was common for both Denmark, Sweden and Finland. This could suggest differences in the virulence or in modes of transmission of predominating and rare types of S. aureus associated with bovine mastitis....

Microbial community responses to 17 years of altered precipitation are seasonally dependent and coupled to co-varying effects of water content on vegetation and soil C

Science.gov (United States)

Sorensen, Patrick O.; Germino, Matthew J.; Feris, Kevin P.

2013-01-01

Precipitation amount and seasonal timing determine the duration and distribution of water available for plant and microbial activity in the cold desert sagebrush steppe. In this study, we sought to determine if a sustained shift in the amount and timing of precipitation would affect soil microbial diversity, community composition, and soil carbon (C) storage. Field plots were irrigated (+200 mm) during the dormant or growing-season for 17 years. Microbial community responses were assessed over the course of a year at two depths (15–20 cm, 95–100 cm) by terminal restriction fragment length polymorphism (T-RFLP), along with co-occurring changes in plant cover and edaphic properties. Bacterial richness, Shannon Weaver diversity, and composition in shallow soils (15–20 cm) as well as evenness in deep soils (95–100 cm) differed across irrigation treatments during July. Irrigation timing affected fungal community diversity and community composition during the dormant season and most strongly in deep soils (95–100 cm). Dormant-season irrigation increased the ratio of shrubs to forbs and reduced soil C in shallow soils by 16% relative to ambient conditions. It is unclear whether or not soil C will continue to decline with continued treatment application or if microbial adaptation could mitigate sustained soil C losses. Future changes in precipitation timing will affect soil microbes in a seasonally dependent manner and be coupled to co-varying effects of water content on vegetation and soil C.

Seasonal Variation in Soil Microbial Biomass, Bacterial Community Composition and Extracellular Enzyme Activity in Relation to Soil Respiration in a Northern Great Plains Grassland

Science.gov (United States)

Wilton, E.; Flanagan, L. B.

2014-12-01

Soil respiration rate is affected by seasonal changes in temperature and moisture, but is this a direct effect on soil metabolism or an indirect effect caused by changes in microbial biomass, bacterial community composition and substrate availability? In order to address this question, we compared continuous measurements of soil and plant CO2 exchange made with an automatic chamber system to analyses conducted on replicate soil samples collected on four dates during June-August. Microbial biomass was estimated from substrate-induced respiration rate, bacterial community composition was determined by 16S rRNA amplicon pyrosequencing, and β-1,4-N-acetylglucosaminidase (NAGase) and phenol oxidase enzyme activities were assayed fluorometrically or by absorbance measurements, respectively. Soil microbial biomass declined from June to August in strong correlation with a progressive decline in soil moisture during this time period. Soil bacterial species richness and alpha diversity showed no significant seasonal change. However, bacterial community composition showed a progressive shift over time as measured by Bray-Curtis dissimilarity. In particular, the change in community composition was associated with increasing relative abundance in the alpha and delta classes, and declining abundance of the beta and gamma classes of the Proteobacteria phylum during June-August. NAGase showed a progressive seasonal decline in potential activity that was correlated with microbial biomass and seasonal changes in soil moisture. In contrast, phenol oxidase showed highest potential activity in mid-July near the time of peak soil respiration and ecosystem photosynthesis, which may represent a time of high input of carbon exudates into the soil from plant roots. This input of exudates may stimulate the activity of phenol oxidase, a lignolytic enzyme involved in the breakdown of soil organic matter. These analyses indicated that seasonal change in soil respiration is a complex

Ribotyping and whole-cell protein analysis of spirochetes isolated from arthropods in the Czech Republic

Czech Academy of Sciences Publication Activity Database

Buňková, L.; Švec, P.; Halouzka, Jiří; Rudolf, Ivo; Němec, M.

2008-01-01

Roč. 15, č. 2 (2008), s. 225-230 ISSN 1232-1966 R&D Projects: GA AV ČR KJB600930613; GA ČR GA206/03/0726 Institutional research plan: CEZ:AV0Z60930519 Keywords : Borrelia burgdorferi sensu lato * Czech Republic * ribotyping * whole-cell protein analysis * taxonomy Subject RIV: EE - Microbiology, Virology Impact factor: 1.443, year: 2008 http://www.aaem.pl/pdf/15225.pdf

Effects of application of corn straw on soil microbial community structure during the maize growing season.

Science.gov (United States)

Lu, Ping; Lin, Yin-Hua; Yang, Zhong-Qi; Xu, Yan-Peng; Tan, Fei; Jia, Xu-Dong; Wang, Miao; Xu, De-Rong; Wang, Xi-Zhuo

2015-01-01

This study investigated the influence of corn straw application on soil microbial communities and the relationship between such communities and soil properties in black soil. The crop used in this study was maize (Zea mays L.). The five treatments consisted of applying a gradient (50, 100, 150, and 200%) of shattered corn straw residue to the soil. Soil samples were taken from May through September during the 2012 maize growing season. The microbial community structure was determined using phospholipid fatty acid (PLFA) analysis. Our results revealed that the application of corn straw influenced the soil properties and increased the soil organic carbon and total nitrogen. Applying corn straw to fields also influenced the variation in soil microbial biomass and community composition, which is consistent with the variations found in soil total nitrogen (TN) and soil respiration (SR). However, the soil carbon-to-nitrogen ratio had no effect on soil microbial communities. The abundance of PLFAs, TN, and SR was higher in C1.5 than those in other treatments, suggesting that the soil properties and soil microbial community composition were affected positively by the application of corn straw to black soil. A Principal Component Analysis indicated that soil microbial communities were different in the straw decomposition processes. Moreover, the soil microbial communities from C1.5 were significantly different from those of CK (p soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p soil properties and soil microbial communities and that these properties affect these communities. The individual PLFA signatures were sensitive indicators that reflected the changes in the soil environment condition. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Influence of an oyster reef on development of the microbial heterotrophic community of an estuarine biofilm.

Science.gov (United States)

Nocker, Andreas; Lepo, Joe E; Snyder, Richard A

2004-11-01

We characterized microbial biofilm communities developed over two very closely located but distinct benthic habitats in the Pensacola Bay estuary using two complementary cultivation-independent molecular techniques. Biofilms were grown for 7 days on glass slides held in racks 10 to 15 cm over an oyster reef and an adjacent muddy sand bottom. Total biomass and optical densities of dried biofilms showed dramatic differences for oyster reef versus non-oyster reef biofilms. This study assessed whether the observed spatial variation was reflected in the heterotrophic prokaryotic species composition. Genomic biofilm DNA from both locations was isolated and served as a template to amplify 16S rRNA genes with universal eubacterial primers. Fluorescently labeled PCR products were analyzed by terminal restriction fragment length polymorphism, creating a genetic fingerprint of the composition of the microbial communities. Unlabeled PCR products were cloned in order to construct a clone library of 16S rRNA genes. Amplified ribosomal DNA restriction analysis was used to screen and define ribotypes. Partial sequences from unique ribotypes were compared with existing database entries to identify species and to construct phylogenetic trees representative of community structures. A pronounced difference in species richness and evenness was observed at the two sites. The biofilm community structure from the oyster reef setting had greater evenness and species richness than the one from the muddy sand bottom. The vast majority of the bacteria in the oyster reef biofilm were related to members of the gamma- and delta-subdivisions of Proteobacteria, the Cytophaga-Flavobacterium -Bacteroides cluster, and the phyla Planctomyces and Holophaga-Acidobacterium. The same groups were also present in the biofilm harvested at the muddy sand bottom, with the difference that nearly half of the community consisted of representatives of the Planctomyces phylum. Total species richness was estimated

Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought.

Science.gov (United States)

Mark Ibekwe, A; Ors, Selda; Ferreira, Jorge F S; Liu, Xuan; Suarez, Donald L

2017-02-01

Salinity is a common problem under irrigated agriculture, especially in low rainfall and high evaporative demand areas of southwestern United States and other semi-arid regions around the world. However, studies on salinity effects on soil microbial communities are relatively few while the effects of irrigation-induced salinity on soil chemical and physical properties and plant growth are well documented. In this study, we examined the effects of salinity, temperature, and temporal variability on soil and rhizosphere microbial communities in sand tanks irrigated with prepared solutions designed to simulate saline wastewater. Three sets of experiments with spinach (Spinacia oleracea L., cv. Racoon) were conducted under saline water during different time periods (early winter, late spring, and early summer). Bacterial 16S V4 rDNA region was amplified utilizing fusion primers designed against the surrounding conserved regions using MiSeq® Illumina sequencing platform. Across the two sample types, bacteria were relatively dominant among three phyla-the Proteobacteria, Cyanobacteria, and Bacteroidetes-accounted for 77.1% of taxa detected in the rhizosphere, while Proteobacteria, Bacteroidetes, and Actinobacteria accounted for 55.1% of taxa detected in soil. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, community structure, and specific bacterial groups in soil and rhizosphere samples. Permutational analysis of variance (PERMANOVA) analysis showed that soil temperature (P=0.001), rhizosphere temperature (P=0.001), rhizosphere salinity (P=0.032), and evapotranspiration (P=0.002) significantly affected beta diversity of soil and rhizosphere microbial communities. Furthermore, salinity had marginal effects (P=0.078) on soil beta diversity. However, temporal variability differentially affected rhizosphere microbial communities irrigated with saline wastewater. Therefore, microbial communities in

Diversity and seasonal fluctuation of predominant microbial communities in Bhitarkanika, a tropical mangrove ecosystem in India

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Rashmi Ranjan Mishra

2012-06-01

Full Text Available Different groups of microorganisms are present in mangrove areas, and they perform complex interactions for nutrient and ecological balances. Since little is known about microbial populations in mangroves, this study analyzed the microbial community structure and function in relation to soil physico-chemical properties in Bhitarkanika, a tropical mangrove ecosystem in India. Spatial and seasonal fluctuations of thirteen important groups of microorganisms were evaluated from the mangrove forest sediments during different seasons, along with soil physico-chemical parameters. The overall microbial load (x10(5cfu/g soil in soil declined in the order of heterotrophic, free living N2 fixing, Gram-negative nitrifying, sulphur oxidizing, Gram-positive, spore forming, denitrifying, anaerobic, phosphate solubilizing, cellulose degrading bacteria, fungi and actinomycetes. Populations of the heterotrophic, phosphate solubilizing, sulphur oxidizing bacteria and fungi were more represented in the rainy season, while, Gram-negative, Gram-positive, nitrifying, denitrifying, cellulose decomposing bacteria and actinomycetes in the winter season. The pool size of most of other microbes either declined or maintained throughout the season. Soil nutrients such as N, P, K (Kg/ha and total C (% contents were higher in the rainy season and they did not follow any common trend of changes throughout the study period. Soil pH and salinity (mS/cm varied from 6-8 and 6.4-19.5, respectively, and they normally affected the microbial population dynamics. Determination of bacterial diversity in Bhitarkanika mangrove soil by culture method showed the predominance of bacterial genera such as Bacillus, Pseudomonas, Desulfotomaculum, Desulfovibrio, Desulfomonas, Methylococcus, Vibrio, Micrococcus, Klebsiella and Azotobacter. Principal component analysis (PCA revealed a correlation among local environmental variables with the sampling locations on the microbial community in the

An Outbreak of Clostridium difficile Ribotype 027 Associated with Length of Stay in the Intensive Care Unit and Use of Selective Decontamination of the Digestive Tract: A Case Control Study.

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Yvette H van Beurden

Full Text Available An outbreak of Clostridium difficile ribotype 027 infection (CDI occurred at an university hospital, involving 19 departments. To determine what hospital-associated factors drove the outbreak of this particular strain we performed a case-control study.Cases (n = 79, diagnosed with CDI due to C. difficile ribotype 027 were matched for age and treating medical specialty to four control patients (n = 316. Patients diagnosed with CDI due to other ribotypes were included as a second control group. A random selection of C. difficile ribotype 027 strains (n = 10 was genotyped by Whole Genome Sequencing (WGS.WGS showed the outbreak was likely caused by a single strain of C. difficile (two or less single-nucleotide variants between isolates. Ninety-five percent of cases had used antibiotics, compared to 56% of controls. Previous admission to the intensive care unit (ICU (OR: 2.4, 95% CI 1.0-5.6, longer length of stay (LOS, and recent hospital admission were associated with CDI ribotype 027. Cases were less likely to have been admitted to a ward with a known isolated CDI patient (OR: 0.2, 95% CI 0.1-0.6. Analysis of patients who stayed at the ICU (35 cases; 51 controls, indicated that the use of selective decontamination of the digestive tract (SDD and a longer LOS in the ICU were associated with CDI risk.In this large outbreak, any antibiotic use, including SDD use, appeared as a prerequisite for acquisition of the outbreak strain. The role of use of SDD and prolonged stay on the ICU could not be disentangled, but both factors can play a biologically plausible role in C. difficile acquisition and infection.

PCR ribotype prevalence and molecular basis of macrolide-lincosamide-streptogramin B (MLSB) and fluoroquinolone resistance in Irish clinical Clostridium difficile isolates.

LENUS (Irish Health Repository)

Solomon, Katie

2011-09-01

Antimicrobial use is recognized as a risk factor for Clostridium difficile infection (CDI) and outbreaks. We studied the relationship between PCR ribotype, antimicrobial susceptibility and the genetic basis of resistance in response to exposure to antimicrobial agents.

Clostridium difficile infection among immunocompromised patients in Rio de Janeiro, Brazil and detection of moxifloxacin resistance in a ribotype 014 strain.

Science.gov (United States)

Secco, Danielle Angst; Balassiano, Ilana Teruszkin; Boente, Renata Ferreira; Miranda, Karla Rodrigues; Brazier, Jon; Hall, Val; dos Santos-Filho, Joaquim; Lobo, Leandro Araujo; Nouér, Simone Aranha; Domingues, Regina Maria Cavalcanti Pilotto

2014-08-01

Clostridium difficile is a Gram-positive spore forming anaerobic bacterium, often associated with nosocomial diarrhea and pseudomembranous colitis. The acquisition of this organism occurs primarily in hospitals through accidental ingestion of spores, and its establishment and proliferation in the colon results from the removal of members of the normal intestinal flora during or after antibiotic therapy. In this study, stool samples from patients admitted to the University Hospital Clementino Fraga Filho (HUCCF/UFRJ) were screened for C. difficile toxins with an ELISA test and cultured with standard techniques for C. difficile isolation. A total of 74 stool samples were collected from patients undergoing antibiotic therapy between August 2009 and November 2010, only two (2.7%) were positive in the ELISA test and culture. A third isolate was obtained from a negative ELISA test sample. All cases of CDI were identified in patients with acute lymphoid or myeloid leukemia. Genotypic and phenotypic characterization showed that all strains carried toxins A and B genes, and belonged to PCR-ribotypes 014, 043 and 046. The isolated strains were sensitive to metronidazole and vancomycin, and resistant to ciprofloxacin and levofloxacin. Resistance to moxifloxacin, was present in the strain from PCR-ribotype 014, that showed an amino acid substitution in gyrB gene (Asp 426 → Asn). This is the first time that this mutation in a PCR-ribotype 014 strain has been described in Brazil. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ribotype 078 Clostridium difficile infection incidence in Dutch hospitals is not associated with provincial pig farming: Results from a national sentinel surveillance, 2009-2015.

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Sofie M van Dorp

Full Text Available It has been suggested that the high incidence of ribotype 078 Clostridium difficile infections (CDI in the Netherlands is related to pig farming.We used data of hospitalised CDI patients (>2yrs of age diagnosed between May 2009 and May 2015 in 26 hospitals participating in a national sentinel surveillance. We compared clinical and geographical characteristics of 078 CDI to other CDI. We investigated the association between 078 CDI incidence and four indicators of pig farming (piglet, pig, piglet farm and pig farm density by mixed-effects Poisson regression. We used a space-time permutation model to search for community-onset 078 CDI clusters (using SaTScan.A total of 4,691 CDI were identified. Ribotype 078 was isolated in 493 of 3,756 patients (13.1% including a typing result. These patients had slightly higher community-onset disease and a 35% increase of 30-day mortality compared to non-078 CDI patients. The pooled overall and 078 incidence rates were 2.82 (95% CI, 2.42-3.29 and 0.26 (95% CI, 0.21-0.31 CDI per 10,000 patients-days respectively. Hospital 078 CDI incidence was not associated with provincial pig (IRR, 0.98; 95% CI, 0.89-1.08, piglet (IRR, 0.95; 95% CI, 0.75-1.19, pig farm (IRR, 1.08; 95% CI, 0.84-1.39, or piglet farm density (IRR, 1.00; 95% CI, 0.56-1.79. No clusters of community-onset ribotype 078 CDI were found.Our results do not indicate that the ribotype 078 CDI incidence in hospitals is related to pig (farm or piglet (farm density. However, transmission beyond provincial borders or in non-hospitalised patients cannot be excluded.

Seasonal variations of microbial community in a full scale oil field produced water treatment plant

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Q. Xie

2016-01-01

Full Text Available This study investigated the microbial community in a full scale anaerobic baffled reactor and sequencing batch reactor system for oil-produced water treatment in summer and winter. The community structures of fungi and bacteria were analyzed through polymerase chain reaction–denaturing gradient gel electrophoresis and Illumina high-throughput sequencing, respectively. Chemical oxygen demand effluent concentration achieved lower than 50 mg/L level after the system in both summer and winter, however, chemical oxygen demand removal rates after anaerobic baffled reactor treatment system were significant higher in summer than that in winter, which conformed to the microbial community diversity. Saccharomycotina, Fusarium, and Aspergillus were detected in both anaerobic baffled reactor and sequencing batch reactor during summer and winter. The fungal communities in anaerobic baffled reactor and sequencing batch reactor were shaped by seasons and treatment units, while there was no correlation between abundance of fungi and chemical oxygen demand removal rates. Compared to summer, the total amount of the dominant hydrocarbon degrading bacteria decreased by 10.2% in anaerobic baffled reactor, resulting in only around 23% of chemical oxygen demand was removed in winter. Although microbial community significantly varied in the three parallel sulfide reducing bacteria, the performance of these bioreactors had no significant difference between summer and winter.

Seasonal variations of microbial community in a full scale oil field produced water treatment plant

International Nuclear Information System (INIS)

Xie, Q.; Bai, S.; Li, Y.; Liu, L.; Wang, S.; Xi, J.

2016-01-01

This study investigated the microbial community in a full scale anaerobic baffled reactor and sequencing batch reactor system for oil-produced water treatment in summer and winter. The community structures of fungi and bacteria were analyzed through polymerase chain reaction–denaturing gradient gel electrophoresis and Illumina high throughput sequencing, respectively. Chemical oxygen demand effluent concentration achieved lower than 50 mg/L level after the system in both summer and winter, however, chemical oxygen demand removal rates after anaerobic baffled reactor treatment system were significant higher in summer than that in winter, which conformed to the microbial community diversity. Saccharomycotina, Fusarium, and Aspergillus were detected in both anaerobic baffled reactor and sequencing batch reactor during summer and winter. The fungal communities in anaerobic baffled reactor and sequencing batch reactor were shaped by seasons and treatment units, while there was no correlation between abundance of fungi and chemical oxygen demand removal rates. Compared to summer, the total amount of the dominant hydrocarbon degrading bacteria decreased by 10.2% in anaerobic baffled reactor, resulting in only around 23% of chemical oxygen demand was removed in winter. Although microbial community significantly varied in the three parallel sulfide reducing bacteria, the performance of these bioreactors had no significant difference between summer and winter.

Routine disc diffusion antimicrobial susceptibility testing of Clostridium difficile and association with PCR ribotype 027

DEFF Research Database (Denmark)

Holt, H M; Danielsen, T K; Justesen, U S

2015-01-01

Reduced susceptibility to metronidazole and vancomycin in Clostridium difficile has been reported, which emphasises the need for simple antimicrobial susceptibility testing methods. The aim of this study was to apply a published disc diffusion method and zone diameter breakpoint correlates...... the published breakpoint (difficile PCR ribotype 027 isolates had smaller zone...... diameters than non-027 isolates. The disc diffusion method is very simple and inexpensive, and the published zone diameter breakpoints will detect C. difficile isolates with reduced susceptibility to metronidazole and vancomycin....

The Recent Emergence of Clostridium difficile Infection in Romanian Hospitals is Associated with a High Prevalence of Polymerase Chain Reaction Ribotype 027.

Science.gov (United States)

Popescu, Gabriel Adrian; Serban, Roxana; Pistol, Adriana; Niculcea, Andreea; Preda, Andreea; Lemeni, Daniela; Macovei, Ioana Sabina; Tălăpan, Daniela; Rafila, Alexandru; Florea, Dragoş

2018-03-15

To investigate the epidemiology of Clostridium difficile infection in Romanian hospitals. A survey was conducted at nine hospitals throughout Romania between November 2013 and February 2014. The survey identified 393 patients with Clostridium difficile infection. The median age was 67 years (range: 2-94 years); 56% of patients were aged >65 years. The mean prevalence of Clostridium difficile infection was 5.2 cases per 10.000 patient-days. The highest prevalences were 24.9 and 20 per 10.000 patient-days in hospitals specializing in gastroenterology and infectious diseases, respectively. Clostridium difficile infections were health care-associated in 70.5% patients and community-acquired in 10.2%. The origin was not determined in 19.3%. Clostridium difficile infection was severe in 12.3% of patients, and the in-hospital all-cause mortality was 8.8%. Polymerase chain reaction ribotype 027 had the highest prevalence in all participating hospitals and represented 82.6% of the total ribotyped isolates. The minimum inhibitory concentration of moxifloxacin was >4 μg/mL for 59 of 80 tested isolates (73.8%). Of 59 isolates, 54 were highly resistant to moxifloxacin (minimum inhibitory concentration ≥32 μg/mL), and the majority were polymerase chain reaction ribotype 027 (pClostridium difficile infections in Romania. In some specialized hospitals, the prevalence of Clostridium difficile infection was higher than the European mean prevalence, and this demonstrates the need for strict adherence to infection control programs.

Seasonal variations and effects of nutrient applications on N and P and microbial biomass under two temperate heathland plants

DEFF Research Database (Denmark)

Nielsen, Pia Lund; Andresen, Louise Christoffersen; Michelsen, Anders

2009-01-01

. The microbial biomass on the other hand was positively related to soil water content in fertilized plots indicating that this was due to an indirect effect of enhanced nutrient availability. Microbial N and P pools were respectively 1000 and 100 times higher than the pool of inorganic N and P, and microbes...... this process. In this study the soil properties under two dominant heathland plants, the dwarf shrub Calluna vulgaris and the grass Deschampsia flexuosa, were investigated, with focus on nutrient content in the organic top soil and soil microbes during the main growing season and effects of nutrient amendments...... therefore may play an important role in regulating plant nutrient supply. Judged from responses of inorganic and microbial N and P concentrations to added N and P, N seemed to limit C. vulgaris and soil microbes below while P seemed to limit D. flexuosa and soil microbes below this species. There were lower...

Long-chain fatty acids inhibition and adaptation process in anaerobic thermophilic digestion: Batch tests, microbial community structure and mathematical modelling

DEFF Research Database (Denmark)

Paltsi, Jordi; Illa, J.; Prenafeta-Boldu, F.X.

2010-01-01

Biomass samples taken during the continuous operation of thermophilic anaerobic digestors fed with manure and exposed to successive inhibitory pulses of long-chain fatty acids (LCFA) were characterized in terms of specific metabolic activities and 16S rDNA DGGE profiling of the microbial community....... Population profiles of eubacterial and archaeal 16S rDNA genes revealed that no significant shift on microbial community composition took place upon biomass exposure to LCFA. DNA sequencing of predominant DGGE bands showed close phylogenetic affinity to ribotypes characteristic from specific beta...... kinetics considering the relation between LCFA inhibitory substrate concentration and specific biomass content, as an approximation to the adsorption process, improved the model fitting and provided a better insight on the physical nature of the LCFA inhibition process. (C) 2009 Elsevier Ltd. All rights...

COMPOSITION AND FUNCTION OF THE MICROBIAL COMMUNITY RELATED WITH THE NITROGEN CYCLING ON THE POTATO RHIZOSPHERE

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Nathalia Maria Vanesa Florez Zapata

2013-09-01

Full Text Available In the S. tuberosum group phureja crops, mineral fertilizer and organic amendments are applied to meet the plants’ nutritional demands, however the effect of such practices on the associated rizospheric microbial communities are still unknown. Nitrogen plays an important role in agricultural production, and a great diversity of microorganisms regulates its transformation in the soil, affecting its availability for the plant. The aim of this study was to assess the structure of microbal[trm1]  communities related with the N cycle of S. tuberosum group phureja  rizospheric soil samples, with contrasting physical-chemical properties and fertilization strategy.  Few significant differences between the community composition at the phylum level were found, only Planctomycetes phylum was different between samples of different soil type and fertilization strategy. However, the analysis of nitrogen-associated functional groups made by ribotyping characterization, grouped soils in terms of such variables in a similar way to the physical-chemical properties. Major differences between soil samples were typified by higher percentages of the ribotypes from nitrite oxidation, nitrogen fixation and denitrification on organic amendment soils. Our results suggest that, the dominant rhizosphere microbial composition is very similar between soils, possibly as a result of population’s selection mediated by the rhizosphere effect. However, agricultural management practices in addition to edaphic properties of sampled areas, appear to affect some functional groups associated with the nitrogen cycling, due to differences found on soil’s physical-chemical properties, like the concentration of ammonium that seems to have an effect regulating the distribution and activity of nitrogen related functional groups in the S. tuberosum rhizosphere.

Seasonal Variations of Indoor Microbial Exposures and Their Relation to Temperature, Relative Humidity, and Air Exchange Rate

DEFF Research Database (Denmark)

Frankel, Mika; Bekö, Gabriel; Timm, Michael

2012-01-01

with temperature, relative humidity, and air exchange rates in Danish homes. Airborne inhalable dust was sampled in five Danish homes throughout the four seasons of 1 year (indoors, n = 127; outdoors, n = 37). Measurements included culturable fungi and bacteria, endotoxin, N-acetyl-beta-d-glucosaminidase, total...... inflammatory potential, particles (0.75 to 15 μm), temperature, relative humidity, and air exchange rates. Significant seasonal variation was found for all indoor microbial exposures, excluding endotoxin. Indoor fungi peaked in summer (median, 235 CFU/m3) and were lowest in winter (median, 26 CFU/m3). Indoor...... of inhalable dust and number of particles. Temperature and air exchange rates were positively associated with fungi and N-acetyl-beta-d-glucosaminidase and negatively with bacteria and the total inflammatory potential. Although temperature, relative humidity, and air exchange rates were significantly...

Seasonal microbial and nutrient responses during a 5-year reduction in the daily temperature range of soil in a Chihuahuan Desert ecosystem.

Science.gov (United States)

van Gestel, Natasja C; Dhungana, Nirmala; Tissue, David T; Zak, John C

2016-01-01

High daily temperature range of soil (DTRsoil) negatively affects soil microbial biomass and activity, but its interaction with seasonal soil moisture in regulating ecosystem function remains unclear. For our 5-year field study in the Chihuahuan Desert, we suspended shade cloth 15 cm above the soil surface to reduce daytime temperature and increase nighttime soil temperature compared to unshaded plots, thereby reducing DTRsoil (by 5 ºC at 0.2 cm depth) without altering mean temperatures. Microbial biomass production was primarily regulated by seasonal precipitation with the magnitude of the response dependent on DTRsoil. Reduced DTRsoil more consistently increased microbial biomass nitrogen (MBN; +38%) than microbial biomass carbon (MBC) with treatment responses being similar in spring and summer. Soil respiration depended primarily on soil moisture with responses to reduced DTRsoil evident only in wetter summer soils (+53%) and not in dry spring soils. Reduced DTRsoil had no effect on concentrations of dissolved organic C, soil organic matter (SOM), nor soil inorganic N (extractable NO3 (-)-N + NH4 (+)-N). Higher MBN without changes in soil inorganic N suggests faster N cycling rates or alternate sources of N. If N cycling rates increased without a change to external N inputs (atmospheric N deposition or N fixation), then productivity in this desert system, which is N-poor and low in SOM, could be negatively impacted with continued decreases in daily temperature range. Thus, the future N balance in arid ecosystems, under conditions of lower DTR, seems linked to future precipitation regimes through N deposition and regulation of soil heat load dynamics.

Comparison of ribotyping, randomly amplified polymorphic DNA analysis, and pulsed-field gel electrophoresis in typing of Lactobacillus rhamnosus and L. casei strains.

Science.gov (United States)

Tynkkynen, S; Satokari, R; Saarela, M; Mattila-Sandholm, T; Saxelin, M

1999-09-01

A total of 24 strains, biochemically identified as members of the Lactobacillus casei group, were identified by PCR with species-specific primers. The same set of strains was typed by randomly amplified polymorphic DNA (RAPD) analysis, ribotyping, and pulsed-field gel electrophoresis (PFGE) in order to compare the discriminatory power of the methods. Species-specific primers for L. rhamnosus and L. casei identified the type strain L. rhamnosus ATCC 7469 and the neotype strain L. casei ATCC 334, respectively, but did not give any signal with the recently revived species L. zeae, which contains the type strain ATCC 15820 and the strain ATCC 393, which was previously classified as L. casei. Our results are in accordance with the suggested new classification of the L. casei group. Altogether, 21 of the 24 strains studied were identified with the species-specific primers. In strain typing, PFGE was the most discriminatory method, revealing 17 genotypes for the 24 strains studied. Ribotyping and RAPD analysis yielded 15 and 12 genotypes, respectively.

Antimicrobial resistance and PCR-ribotyping of Shigella responsible for foodborne outbreaks occurred in southern Brazil

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Cheila Minéia Daniel de Paula

2010-12-01

Full Text Available Little information about Shigella responsible for foodborne shigellosis is available in Brazil. The present study aimed to investigate the antimicrobial resistance and PCR-ribotyping patterns of Shigella isolates responsible for foodborne outbreaks occurred in Rio Grande do Sul State (RS, Southern Brazil in the period between 2003 and 2007. Shigella strains (n=152 were isolated from foods and fecal samples of victims of shigellosis outbreaks investigated by the Surveillance Service. Identification of the strains at specie level indicated that 71.1% of them were S. flexneri, 21.5% S. sonnei, and 0.7% S. dysenteriae. Ten strains (6.7% were identified only as Shigella spp. An increasing occurrence of S. sonnei was observed after 2004. Most of the strains were resistant to streptomycin (88.6%, followed by ampicillin (84.6%, and sulfamethoxazole/trimethoprim (80.5 %. Resistant strains belonged to 73 patterns, and pattern A (resistance to ampicillin, sulfamethoxazole/trimethoprim, tetracycline, streptomycin, chloramphenicol, and intermediate resistance to kanamycin grouped the largest number of isolates (n=36. PCR-ribotyping identified three banding patterns (SH1, SH2, and SH3. SH1 grouped all S. flexneri and SH2 grouped all S. sonnei. The S. dysenteriae strain belonged to group SH3. According to the results, several Shigella isolates shared the same PCR-rybotyping banding pattern and the same resistance profile, suggesting that closely related strains were responsible for the outbreaks. However, other molecular typing methods need to be applied to confirm the clonal relationship of these isolates.

Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters.

Science.gov (United States)

de Menezes, Alexandre B; Prendergast-Miller, Miranda T; Richardson, Alan E; Toscas, Peter; Farrell, Mark; Macdonald, Lynne M; Baker, Geoff; Wark, Tim; Thrall, Peter H

2015-08-01

Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community terminal restriction length polymorphisms as well as soil properties in paired woodland and pasture sites. Canonical correspondence analysis (CCA) revealed that shifts in woodland community composition correlated with soil dissolved organic carbon, while changes in pasture community composition correlated with moisture, nitrogen and phosphorus. Weighted correlation network analysis detected two distinct microbial modules per land use. Bacterial and fungal ribotypes did not group separately, rather all modules comprised of both bacterial and fungal ribotypes. Woodland modules had a similar fungal : bacterial ribotype ratio, while in the pasture, one module was fungal dominated. There was no correspondence between pasture and woodland modules in their ribotype composition. The modules had different relationships to soil variables, and these contrasts were not detected without the use of network analysis. This study demonstrated that fungi and bacteria, components of the soil microbial communities usually treated as separate functional groups as in a CCA approach, were co-correlated and formed distinct associations in these adjacent habitats. Understanding these distinct modular associations may shed more light on their niche space in the soil environment, and allow a more realistic description of soil microbial ecology and function. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Seasonal variability in the persistence of dissolved environmental DNA (eDNA in a marine system: The role of microbial nutrient limitation.

Directory of Open Access Journals (Sweden)

Ian Salter

Full Text Available Environmental DNA (eDNA can be defined as the DNA pool recovered from an environmental sample that includes both extracellular and intracellular DNA. There has been a significant increase in the number of recent studies that have demonstrated the possibility to detect macroorganisms using eDNA. Despite the enormous potential of eDNA to serve as a biomonitoring and conservation tool in aquatic systems, there remain some important limitations concerning its application. One significant factor is the variable persistence of eDNA over natural environmental gradients, which imposes a critical constraint on the temporal and spatial scales of species detection. In the present study, a radiotracer bioassay approach was used to quantify the kinetic parameters of dissolved eDNA (d-eDNA, a component of extracellular DNA, over an annual cycle in the coastal Northwest Mediterranean. Significant seasonal variability in the biological uptake and turnover of d-eDNA was observed, the latter ranging from several hours to over one month. Maximum uptake rates of d-eDNA occurred in summer during a period of intense phosphate limitation (turnover <5 hrs. Corresponding increases in bacterial production and uptake of adenosine triphosphate (ATP demonstrated the microbial utilization of d-eDNA as an organic phosphorus substrate. Higher temperatures during summer may amplify this effect through a general enhancement of microbial metabolism. A partial least squares regression (PLSR model was able to reproduce the seasonal cycle in d-eDNA persistence and explained 60% of the variance in the observations. Rapid phosphate turnover and low concentrations of bioavailable phosphate, both indicative of phosphate limitation, were the most important parameters in the model. Abiotic factors such as pH, salinity and oxygen exerted minimal influence. The present study demonstrates significant seasonal variability in the persistence of d-eDNA in a natural marine environment that can

Differentiation of Shewanella putrefaciens and Shewanella alga on the basis of whole-cell protein profiles, ribotyping, phenotypic characterization, and 16S rRNA gene sequence analysis

DEFF Research Database (Denmark)

Vogel, Birte Fonnesbech; Jørgensen, K.; Christensen, H.

1997-01-01

Seventy-six presumed Shewanella putrefaciens isolates from fish, oil drillings, and clinical specimens, the type strain of Shewanella putrefaciens (ATCC 8071), the type strain of Shewanella alga (IAM 14159), and the type strain of Shewanella hanedai (ATCC 33224) were compared by several typing...... methods. Numerical analysis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell protein and ribotyping patterns showed that the strains were separated into two distinct clusters with 56% +/- 10% and 40% +/- 14% similarity for whole- cell protein profiling and ribotyping......, respectively. One cluster consisted of 26 isolates with 52 to 55 mol% G + C and included 15 human isolates, mostly clinical specimens, 8 isolates from marine waters, and the type strain of S. alga. This homogeneous cluster of mesophilic, halotolerant strains was by all analyses identical to the recently...

Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria

Science.gov (United States)

Zwirglmaier, Katrin; Keiz, Katharina; Engel, Marion; Geist, Juergen; Raeder, Uta

2015-01-01

The Osterseen Lake District in Bavaria consists of 19 small interconnected lakes that exhibit a pronounced trophic gradient from eutrophic to oligotrophic. It therefore presents a unique model system to address ecological questions regarding niche adaptation and Baas Becking's long standing hypothesis of “everything is everywhere, but the environment selects.” Here, we present the first assessment of the microbial diversity in these lakes. We sampled the lakes in August and December and used 454 pyrosequencing of 16S rRNA amplicons to analyze the microbial diversity. The diversity patterns between lakes and seasons were compared and the bacterial community composition was correlated with key chemical and physical parameters. Distinct patterns of bacterial diversity only emerged at the level of individual OTUs (operational taxonomic units), but not at the level of the major bacterial phyla. This emphasizes the high functional and physiological diversity among bacterial species within a phylum and calls for analysis of biodiversity at the level of OTUs in order to understand fine-scale biogeography. We were able to identify a number of cosmopolitan OTUs as well as specialist OTUs that were restricted to certain lakes or seasons, suggesting adaptation to specific ecological niches. PMID:26579082

Comparative ribotyping of Staphylococcus intermedius isolated from members of the Canoidea gives possible evidence for host-specificity and co-evolution of bacteria and hosts

DEFF Research Database (Denmark)

Aarestrup, Frank Møller

2001-01-01

A total of 41 Staphylococcus intermedius isolates were isolated from skin of healthy members of six phylogenetic groups within the Canoidea (the dog family, skunk subfamily, weasel subfamily, racoon family, red panda and bear family) of different geographical origin and compared by EcoRI ribotyping...

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre.

Science.gov (United States)

Bryant, Jessica A; Aylward, Frank O; Eppley, John M; Karl, David M; Church, Matthew J; DeLong, Edward F

2016-06-01

Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces.

Cost analysis of an outbreak of Clostridium difficile infection ribotype 027 in a Dutch tertiary care centre.

Science.gov (United States)

van Beurden, Y H; Bomers, M K; van der Werff, S D; Pompe, E A P M; Spiering, S; Vandenbroucke-Grauls, C M J E; Mulder, C J J

2017-04-01

The economic impact of Clostridium difficile infection (CDI) on the healthcare system is significant. From May 2013 to May 2014, an outbreak of C. difficile ribotype 027 occurred in a Dutch tertiary care hospital, involving 72 patients. The primary aim of this study was to provide insight into the financial burden that this CDI outbreak brought upon this hospital. A retrospective analysis was performed to estimate the costs of a one-year-long C. difficile ribotype 027 outbreak. Medical charts were reviewed for patient data. In addition, all costs associated with the outbreak control measures were collected. The attributable costs of the whole outbreak were estimated to be €1,222,376. The main contributing factor was missed revenue due to increased length of stay of CDI patients and closure of beds to enable contact isolation of CDI patients (36%). A second important cost component was extra surveillance and activities of the Department of Medical Microbiology and Infection Control (25%). To the authors' knowledge, this is the first study to provide insight into the attributable costs of CDI in an outbreak setting, and to delineate the major cost items. It is clear that the economic consequences of CDI are significant. The high costs associated with a CDI outbreak should help to justify the use of additional resources for CDI prevention and control. Copyright © 2016 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Pyrosequencing reveals diverse microbial community associated with the zoanthid Palythoa australiae from the South China Sea.

Science.gov (United States)

Sun, Wei; Zhang, Fengli; He, Liming; Li, Zhiyong

2014-05-01

Diverse sessile organisms inhabit the coral reef ecosystems, including corals, sponges, and sea anemones. In the past decades, scleractinian corals (Cnidaria, Anthozoa, Scleractinia) and their associated microorganisms have attracted much attention. Zoanthids (Cnidaria, Anthozoa, Zoanthidea) are commonly found in coral reefs. However, little is known about the community structure of zoanthid-associated microbiota. In this study, the microbial community associated with the zoanthid Palythoa australiae in the South China Sea was investigated by 454 pyrosequencing. As a result, 2,353 bacterial, 583 archaeal, and 36 eukaryotic microbial ribotypes were detected, respectively. A total of 22 bacterial phyla (16 formally described phyla and six candidate phyla) were recovered. Proteobacteria was the most abundant group, followed by Chloroflexi and Actinobacteria. High-abundance Rhizobiales and diverse Chloroflexi were observed in the bacterial community. The archaeal population was composed of Crenarchaeota and Euryarchaeota, with Marine Group I as the dominant lineage. In particular, Candidatus Nitrosopumilus dominated the archaeal community. Besides bacteria and archaea, the zoanthid harbored eukaryotic microorganisms including fungi and algae though their diversity was very low. This study provided the first insights into the microbial community associated with P. australiae by 454 pyrosequencing, consequently laid a basis for the understanding of the association of P. australiae-microbes symbioses.

SSU rDNA sequence diversity and seasonally differentiated distribution of nanoplanktonic ciliates in neritic Bohai and Yellow Seas as revealed by T-RFLP.

Science.gov (United States)

Dong, Jun; Shi, Fei; Li, Han; Zhang, Xiaoming; Hu, Xiaozhong; Gong, Jun

2014-01-01

Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution patterns of nanoplanktonic oligotrich and choreotrich (OC) ciliates in surface water of three neritic basins of northern China, the South Yellow Sea (SYS), North Yellow Sea (NYS), and Bohai Sea (BS) in June and November 2011. SSU rRNA gene clone libraries generated from three summertime samples (sites B38, B4 and H8) were analyzed and revealed a large novel ribotype diversity, of which many were low-abundant phylotypes belonging to the subclass Oligotrichia, but divergent from described morphospecies. Based on the data of terminal-restriction fragment length polymorphism (T-RFLP) analysis of all 35 samples, we found that the T-RF richness was generally higher in the SYS than in the BS, and negatively correlated with the molar ratio of P to Si. Overall, multidimensional scaling and permutational multivariate analysis of variance of the community turnover demonstrated a distinct seasonal pattern but no basin-to-basin differentiation across all samples. Nevertheless, significant community differences among basins were recognized in the winter dataset. Mantel tests showed that the environmental factors, P:Si ratio, water temperature and concentration of dissolved oxygen (DO), determined the community across all samples. However, both biogeographic distance and environment shaped the community in winter, with DO being the most important physicochemical factor. Our results indicate that the stoichiometric ratio of P:Si is a key factor, through which the phytoplankton community may be shaped, resulting in a cascade effect on the diversity and community composition of OC nanociliates in the N-rich, Si-limited coastal surface waters, and that the Yellow Sea Warm Current drives the nanociliate community, and possibly the microbial food webs

Analysis of the coral associated bacterial community structures in healthy and diseased corals from off-shore of southern Taiwan.

Science.gov (United States)

Chiou, Shu-Fen; Kuo, Jimmy; Wong, Tit-Yee; Fan, Tung-Yung; Tew, Kwee Siong; Liu, Jong-Kang

2010-07-01

The methods of denaturing gradient gel electrophoresis (DGGE) and DNA sequencing were used to analyze the ribotypes of microbial communities associated with corals. Both healthy and diseased coral of different species were collected at three locations off the southern coast of Taiwan. Ribotyping results suggested that the microbial communities were diverse. The microbial community profiles, even among the same species of corals from different geographical locations, differ significantly. The coral-associated bacterial communities contain many bacteria common to the habitants of various invertebrates. However, some bacteria were unexpected. The presence of some unusual species, such as Staphylococcus, Clostridium and Legionella, associated with corals that were likely the results of human activities. Human activities, such as thermal pollution from the nearby nuclear plant, active fishing and tourism industries in the region might have all contributed to the change in bacterial communities and the death of coral colonies around the region.

Repeatability and reproducibility of ribotyping and its computer interpretation.

Science.gov (United States)

Lefresne, Gwénola; Latrille, Eric; Irlinger, Françoise; Grimont, Patrick A D

2004-04-01

Many molecular typing methods are difficult to interpret because their repeatability (within-laboratory variance) and reproducibility (between-laboratory variance) have not been thoroughly studied. In the present work, ribotyping of coryneform bacteria was the basis of a study involving within-gel and between-gel repeatability and between-laboratory reproducibility (two laboratories involved). The effect of different technical protocols, different algorithms, and different software for fragment size determination was studied. Analysis of variance (ANOVA) showed, within a laboratory, that there was no significant added variance between gels. However, between-laboratory variance was significantly higher than within-laboratory variance. This may be due to the use of different protocols. An experimental function was calculated to transform the data and make them compatible (i.e., erase the between-laboratory variance). The use of different interpolation algorithms (spline, Schaffer and Sederoff) was a significant source of variation in one laboratory only. The use of either Taxotron (Institut Pasteur) or GelCompar (Applied Maths) was not a significant source of added variation when the same algorithm (spline) was used. However, the use of Bio-Gene (Vilber Lourmat) dramatically increased the error (within laboratory, within gel) in one laboratory, while decreasing the error in the other laboratory; this might be due to automatic normalization attempts. These results were taken into account for building a database and performing automatic pattern identification using Taxotron. Conversion of the data considerably improved the identification of patterns irrespective of the laboratory in which the data were obtained.

Listeria monocytogenes in RTE foods marketed in Italy: prevalence and automated EcoRI ribotyping of the isolates.

Science.gov (United States)

Meloni, Domenico; Galluzzo, Pietro; Mureddu, Anna; Piras, Francesca; Griffiths, Mansel; Mazzette, Rina

2009-02-15

The aims of the present study were: (a) to investigate the prevalence and the enumeration of Listeria monocytogenes in 200 samples of ready to eat (RTE) foods of animal and vegetal origin collected from different outlets and processing plants in Sardinia; (b) to characterize the isolates by phenotypical and molecular methods; (c) to analyze a subset of 42 L. monocytogenes by automated EcoRI ribotyping in order to predict the strain's potential virulence for humans. The strains were isolated from: smoked fish products, cooked marinated products, meat products and pre-packaged mixed vegetable salads. Of the samples tested, 22% were positive for Listeria spp. The prevalence of L. monocytogenes was 9.5%, while the level of L. monocytogenes in the positive samples was 93%), belonging to 17 different DuPont Identification Library Codes (DUP-IDs) clones. The Simpson's numerical index of discrimination was 0.911. Cluster analysis pointed out a high similarity among strains isolated from meat, fish, and vegetables of different origin. These results confirmed the existence of a widespread population of L. monocytogenes, characterized by highly related strains existing in different geographical areas. 65% of these strains belonged to lineage II (serotypes 1/2a and 1/2c), subtypes known to be associated with sporadic human listeriosis outbreaks. The remaining 35% of the isolates (serotypes 1/2b, 3b and 4b) were allocated to lineage I and belong to distinct clonal groups (DUP-ID 1038 and 1042), which again have been associated with several outbreaks of human listeriosis. Neither atypical profiles nor lineage III strains were found. EcoRI ribotyping was confirmed as a rapid and reliable method for L. monocytogenes typing, providing useful data for epidemiologic and clonality surveys of L. monocytogenes strains isolated from RTE foods.

Anthropogenic Pollution Impact on Microbial Contamination of Lake ...

African Journals Online (AJOL)

Indicator bacteria were enumerated by membrane filtration while pathogenic bacteria were recovered by broth enrichment of water samples. Microbial load did not differ significantly with season and locations but fecal coliform (FC) had positive significant correlation (r = 0.36*; P < 0.05) with season. Mean total coliform (TC) ...

Comparison of Ribotyping, Randomly Amplified Polymorphic DNA Analysis, and Pulsed-Field Gel Electrophoresis in Typing of Lactobacillus rhamnosus and L. casei Strains

OpenAIRE

Tynkkynen, Soile; Satokari, Reetta; Saarela, Maria; Mattila-Sandholm, Tiina; Saxelin, Maija

1999-01-01

A total of 24 strains, biochemically identified as members of the Lactobacillus casei group, were identified by PCR with species-specific primers. The same set of strains was typed by randomly amplified polymorphic DNA (RAPD) analysis, ribotyping, and pulsed-field gel electrophoresis (PFGE) in order to compare the discriminatory power of the methods. Species-specific primers for L. rhamnosus and L. casei identified the type strain L. rhamnosus ATCC 7469 and the neotype strain L. casei ATCC 33...

Microbial community functional change during vertebrate carrion decomposition.

Directory of Open Access Journals (Sweden)

Jennifer L Pechal

Full Text Available Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects. Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition.

Cellulolytic potential under environmental changes in microbial communities from grassland litter

Directory of Open Access Journals (Sweden)

Renaud eBerlemont

2014-11-01

Full Text Available In many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of two years to place environmental change responses into the context of natural variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and constituted ~18.2% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.

Threatened corals provide underexplored microbial habitats.

Directory of Open Access Journals (Sweden)

Shinichi Sunagawa

2010-03-01

Full Text Available Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these "rare" organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7-49.1% were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under

An overview of physico-chemical mechanisms of biogas production by microbial communities: a step towards sustainable waste management.

Science.gov (United States)

Goswami, Ramansu; Chattopadhyay, Pritam; Shome, Arunima; Banerjee, Sambhu Nath; Chakraborty, Amit Kumar; Mathew, Anil K; Chaudhury, Shibani

2016-06-01

Biogas is a combination of methane, CO 2 , nitrogen, H 2 S and traces of few other gases. Almost any organic waste can be biologically transformed into biogas and other energy-rich organic compounds through the process of anaerobic digestion (AD) and thus helping in sustainable waste management. Although microbes are involved in each step of AD, knowledge about those microbial consortia is limited due to the lack of phylogenetic and metabolic data of predominantly unculturable microorganisms. However, culture-independent methods like PCR-based ribotyping has been successfully employed to get information about the microbial consortia involved in AD. Microbes identified have been found to belong mainly to the bacterial phyla of Proteobacteria, Chloroflexi, Firmicutes and Bacteroidetes. Among the archaeal population, the majority have been found to be methanogens (mainly unculturable), the remaining being thermophilic microbes. Thus, the AD process as a whole could be controlled by regulating the microbial consortia involved in it. Optimization in the feedstock, pH, temperature and other physical parameters would be beneficial for the microbial growth and viability and thus helpful for biogas production in AD. Besides, the biogas production is also dependent upon the activity of several key genes, ion-specific transporters and enzymes, like genes coding for methyl-CoM reductase, formylmethanofuran transferase, formate dehydrogenase present in the microbes. Fishing for these high-efficiency genes will ultimately increase the biogas production and sustain the production plant.

Mangrove succession enriches the sediment microbial community in South China.

Science.gov (United States)

Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

2016-06-06

Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.

Seasonal Shifts in Diet and Gut Microbiota of the American Bison (Bison bison.

Directory of Open Access Journals (Sweden)

Gaddy T Bergmann

Full Text Available North American bison (Bison bison are becoming increasingly important to both grassland management and commercial ranching. However, a lack of quantitative data on their diet constrains conservation efforts and the ability to predict bison effects on grasslands. In particular, we know little about the seasonality of the bison diet, the degree to which bison supplement their diet with eudicots, and how changes in diet influence gut microbial communities, all of which play important roles in ungulate performance. To address these knowledge gaps, we quantified seasonal patterns in bison diet and gut microbial community composition for a bison herd in Kansas using DNA sequencing-based analyses of both chloroplast and microbial DNA contained in fecal matter. Across the 11 sampling dates that spanned 166 days, we found that diet shifted continuously over the growing season, allowing bison to take advantage of the seasonal availability of high-protein plant species. Bison consumed more woody shrubs in spring and fall than in summer, when forb and grass intake predominated. In examining gut microbiota, the bacterial phylum Tenericutes shifted significantly in relative abundance over the growing season. This work suggests that North American bison can continuously adjust their diet with a high reliance on non-grasses throughout the year. In addition, we find evidence for seasonal patterns in gut community composition that are likely driven by the observed dietary changes.

Distribution and seasonality of microbial indicators and thermophilic campylobacters in two freshwater bathing sites on the River Lune in northwest England.

Science.gov (United States)

Obiri-Danso, K; Jones, K

1999-12-01

Two freshwater bathing sites, the Crook O'Lune and the University Boathouse, on the River Lune in the north-west of England, were monitored over a 2 year period for the faecal indicators, faecal coliforms and faecal streptococci, the pathogens, Salmonella and Campylobacter, and compliance with the EU Directive on Bathing Water Quality. Faecal indicator numbers showed no seasonal variation, with numbers in the bathing season similar to those in the non-bathing season. They were consistently above the EU Guideline and Imperative standards so that if the EU Bathing Water Quality Directive (76/160/EEC) were applied, neither site would comply. Faecal indicator numbers in the sediments were an order of magnitude higher than in the overlying water. Campylobacter numbers showed seasonal variation in the water with higher counts in winter than in the summer, although numbers were low. Higher numbers were found in the sediments but there was no seasonal variation. Analysis of various inputs showed that indicators and campylobacters came from a mixture of sources, namely a sewage treatment works, agricultural run-off, streams and mallards. Microbial numbers in the water at the Crook O'Lune, which is closer to the sources of pollution, were twice those at the Boathouse. In the sediments they were six to eight times higher. Faecal coliforms were all identified as Escherichia coli of which 80% were a single biotype. Faecal streptococci were all enterococci of which 55% were E. avium, 38% E. faecalis and 7% E. durans. Salmonella was not isolated from either the water column or the sediments. Campylobacters were mainly Camp. jejuni, followed by Camp. coli, UPTC and Camp. lari.

Mineralogical Control on Microbial Diversity in a Weathered Granite?

Science.gov (United States)

Gleeson, D.; Clipson, N.; McDermott, F.

2003-12-01

Mineral transformation reactions and the behaviour of metals in rock and soils are affected not only by physicochemical parameters but also by biological factors, particularly by microbial activity. Microbes inhabit a wide range of niches in surface and subsurface environments, with mineral-microbe interactions being generally poorly understood. The focus of this study is to elucidate the role of microbial activity in the weathering of common silicate minerals in granitic rocks. A site in the Wicklow Mountains (Ireland) has been identified that consists of an outcrop surface of Caledonian (ca. 400 million years old) pegmatitic granite from which large intact crystals of variably weathered muscovite, plagioclase, K-feldspar and quartz were sampled, together with whole-rock granite. Culture-based microbial approaches have been widely used to profile microbial communities, particularly from copiotrophic environments, but it is now well established that for oligotrophic environments such as those that would be expected on weathering faces, perhaps less than 1% of microbial diversity can be profiled by cultural means. A number of culture-independent molecular based approaches have been developed to profile microbial diversity and community structure. These rely on successfully isolating environmental DNA from a given environment, followed by the use of the polymerase chain reaction (PCR) to amplify the typically small quantities of extracted DNA. Amplified DNA can then be analysed using cloning based approaches as well as community fingerprinting systems such as denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP) and ribosomal intergenic spacer analysis (RISA). Community DNA was extracted and the intergenic spacer region (ITS) between small (16S) and large (23S) bacterial subunit rRNA genes was amplified. RISA fragments were then electrophoresed on a non-denaturing polyacrylamide gel. Banding patterns suggest that

Microbial community analysis of ambient temperature anaerobic digesters

Energy Technology Data Exchange (ETDEWEB)

Ciotola, R. [Ohio State Univ., Columbus, OH (United States). Dept. of Food, Agriculture and Biological Engineering

2010-07-01

This paper reported on a study in which designs for Chinese and Indian fixed-dome anaerobic digesters were modified in an effort to produce smaller and more affordable digesters. While these types of systems are common in tropical regions of developing countries, they have not been used in colder climates because of the low biogas yield during the winter months. Although there is evidence that sufficient biogas production can be maintained in colder temperatures through design and operational changes, there is a lack of knowledge about the seasonal changes in the composition of the microbial communities in ambient temperature digesters. More knowledge is needed to design and operate systems for maximum biogas yield in temperate climates. The purpose of this study was to cultivate a microbial community that maximizes biogas production at psychrophilic temperatures. The study was conducted on a 300 gallon experimental anaerobic digester on the campus of Ohio State University. Culture-independent methods were used on weekly samples collected from the digester in order to examine microbial community response to changes in ambient temperature. Microbial community profiles were established using universal bacterial and archaeal primers that targeted the 16S rRNA gene. In addition to the methanogenic archaea, this analysis also targeted some of the other numerically and functionally important microbial taxa in anaerobic digesters, such as hydrolytic, fermentative, acetogenic and sulfate reducing bacteria. According to preliminary results, the composition of the microbial community shifts with changes in seasonal temperature.

Changes in Microbial Community Structure and Soil Biological Properties in Mined Dune Areas During Re-vegetation.

Science.gov (United States)

Escobar, Indra Elena C; Santos, Vilma M; da Silva, Danielle Karla A; Fernandes, Marcelo F; Cavalcante, Uided Maaze T; Maia, Leonor C

2015-06-01

The aim of this study was to describe the impact of re-vegetation on the restoration of microbial community structure and soil microbiological properties in sand dunes that had been affected by mining activity. Soil samples were collected during the dry and rainy seasons from a chronosequence (1, 9, 21 years) of re-vegetated dunes using a single preserved dune as a reference. The composition of the fatty acid methyl esters and soil microbial properties were evaluated. The results showed that the changes in microbial community structure were related to seasonal variations: biomarkers of Gram-positive bacteria were higher than Gram-negative bacteria during the dry season, showing that this group of organisms is more tolerant to these stressful conditions. The microbial community structure in the natural dune was less affected by seasonal variation compared to the re-vegetated areas, whereas the opposite was observed for microbiological properties. Thus, in general, the proportion of saprobic fungi was higher in the natural dune, whereas Gram-negative bacteria were proportionally more common in the younger areas. Although over time the re-vegetation allows the recovery of the microbial community and the soil functions, these communities and functions are different from those found in the undisturbed areas.

Precipitation effects on microbial pollution in a river: lag structures and seasonal effect modification.

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Andreas Tornevi

Full Text Available BACKGROUND: The river Göta Älv is a source of freshwater for 0.7 million swedes. The river is subject to contamination from sewer systems discharge and runoff from agricultural lands. Climate models projects an increase in precipitation and heavy rainfall in this region. This study aimed to determine how daily rainfall causes variation in indicators of pathogen loads, to increase knowledge of variations in river water quality and discuss implications for risk management. METHODS: Data covering 7 years of daily monitoring of river water turbidity and concentrations of E. coli, Clostridium and coliforms were obtained, and their short-term variations in relation with precipitation were analyzed with time series regression and non-linear distributed lag models. We studied how precipitation effects varied with season and compared different weather stations for predictive ability. RESULTS: Generally, the lowest raw water quality occurs 2 days after rainfall, with poor raw water quality continuing for several more days. A rainfall event of >15 mm/24-h (local 95 percentile was associated with a three-fold higher concentration of E. coli and 30% higher turbidity levels (lag 2. Rainfall was associated with exponential increases in concentrations of indicator bacteria while the effect on turbidity attenuated with very heavy rainfall. Clear associations were also observed between consecutive days of wet weather and decreased water quality. The precipitation effect on increased levels of indicator bacteria was significant in all seasons. CONCLUSIONS: Rainfall elevates microbial risks year-round in this river and freshwater source and acts as the main driver of varying water quality. Heavy rainfall appears to be a better predictor of fecal pollution than water turbidity. An increase of wet weather and extreme events with climate change will lower river water quality even more, indicating greater challenges for drinking water producers, and suggesting better

First Investigation of Microbial Community Composition in the Bridge (Gadeok Channel) between the Jinhae-Masan Bay and the South Sea of Korea

Science.gov (United States)

Lee, Jiyoung; Lim, Jae-Hyun; Park, Junhyung; Youn, Seok-Hyun; Oh, Hyun-Ju; Kim, Ju-Hyoung; Kim, Myung Kyum; Cho, Hyeyoun; Yoon, Joo-Eun; Kim, Soyeon; Markkandan, Kesavan; Park, Ki-Tae; Kim, Il-Nam

2018-02-01

Microbial community composition varies based on seasonal dynamics (summer: strongly stratified water column; autumn: weakly stratified water column; winter: vertically homogeneous water column) and vertical distributions (surface, middle, and bottom depths) in the Gadeok Channel, which is the primary passage to exchange waters and materials between the Jinhae-Masan Bay and the South Sea waters. The microbial community composition was analyzed from June to December 2016 using 16S rRNA gene sequencing. The community was dominated by the phyla Proteobacteria (45%), Bacteroidetes (18%), Cyanobacteria (15%), Verrucomicrobia (6%), and Actinobacteria (6%). Alphaproteobacteria (29%) was the most abundant microbial class, followed by Flavobacteria (15%) and Gammaproteobacteria (15%) in all samples. The composition of the microbial communities was found to vary vertically and seasonally. The orders Flavobacteriales and Stramenopiles showed opposing seasonal patterns; Flavobacteriales was more abundant in August and December while Stramenopiles showed high abundance in June and October at all depths. The genus Synechococcus reached extremely high abundance (14%) in the June surface water column, but was much less abundant in December water columns. Clustering analysis showed that there was a difference in the microbial community composition pattern between the strongly stratified season and well-mixed season. These results indicate that the seasonal dynamics of physicochemical and hydrologic conditions throughout the water column are important parameters in shaping the microbial community composition in the Gadeok Channel.

Phytoplankton biomass and microbial abundances during the spring upwelling season in the coastal area off Concepción, central-southern Chile: Variability around a time series station

Science.gov (United States)

Morales, Carmen E.; Anabalón, Valeria

2012-01-01

In the coastal system off Concepción, time series observations at a fixed station (St. 18) have shown strong seasonal changes in the oceanographic environment of the upper layer (blooms, dominated by microplanktonic diatoms, have usually overshadowed the relevance of the smaller microbial components during upwelling. This study focuses on the variability of oceanographic conditions and their association with the structure of the planktonic community (size fractionated chlorophyll-a and microbial abundances) in the upper layer during the upwelling season, examining the extent to which St. 18 is representative of the coastal system off Concepción during springtime. For this purpose, data from three consecutive springs (2004, 2005, 2006) were compared, which included cruises for all years (8 stations around St. 18) as well as monthly sampling at St. 18. Most of the spatial (submesoscale) variability in chlorophyll-a and the microbial components was not significant, but data dispersion around mean values was high. Water column structure (temperature and salinity) in the upper layer explained a significant fraction (25-65%) of the spatial variability in most of the planktonic components; their responses to oceanographic variability were linear in some cases and non-linear in others. For the most part, St. 18 appears to adequately represent mean oceanographic conditions and the structure of planktonic communities in the coastal waters off Concepción during springtime, however spatial variability needs to be taken into account in the interpretations of temporal changes at this fixed station as well as in assessments of carbon flow within, and exportation processes from, this upwelling system.

Seasonality of fibrolytic enzyme activity in herbivore microbial ...

African Journals Online (AJOL)

2012-08-21

Aug 21, 2012 ... liberating end-products such as volatile fatty acids. Cellulase enzyme ... All the other common chemicals such as glacial acetic acid, sodium azide .... specific activity was observed among animal species and between seasons ...

Microbial biomass dynamics dominate N cycle responses to warming in a sub-arctic peatland

Science.gov (United States)

Weedon, J. T.; Aerts, R.; Kowalchuk, G. K.; van Bodegom, P. M.

2012-04-01

The balance of primary production and decomposition in sub-arctic peatlands may shift with climate change. Nitrogen availability will modulate this shift, but little is known about the drivers of soil nitrogen dynamics in these environments, and how they are influenced by rising soil temperatures. We used a long-term open top chamber warming experiment in Abisko, Sweden, to test for the interactive effects of spring warming, summer warming and winter snow addition on soil organic and inorganic nitrogen fluxes, potential activities of carbon and nitrogen cycle enzymes, and the structure of the soil-borne microbial communities. Summer warming increased the flux of soil organic nitrogen over the growing season, while simultaneously causing a seasonal decrease in microbial biomass, suggesting that N flux is driven by large late-season dieback of microbes. This change in N cycle dynamics was not reflected in any of the measured potential enzyme activities. Moreover, the soil microbial community structure was stable across treatments, suggesting non-specific microbial dieback. To further test whether the observed patterns were driven by direct temperature effects or indirect effects (via microbial biomass dynamics), we conducted follow-up controlled experiments in soil mesocosms. Experimental additions of dead microbial cells had stronger effects on N pool sizes and enzyme activities than either plant litter addition or a 5 °C alteration in incubation temperatures. Peat respiration was positively affected by both substrate addition and higher incubation temperatures, but the temperature-only effect was not sufficient to account for the increases in respiration observed in previous field experiments. We conclude that warming effects on peatland N cycling (and to some extent C cycling) are dominated by indirect effects, acting through alterations to the seasonal flux of microbe-derived organic matter. We propose that climate change models of soil carbon and nitrogen

Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics

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Carlo Berg

2018-02-01

Full Text Available Marine and brackish surface waters are highly dynamic habitats that undergo repeated seasonal variations in microbial community composition and function throughout time. While succession of the various microbial groups has been well investigated, little is known about the underlying gene-expression of the microbial community. We investigated microbial interactions via metatranscriptomics over a spring to fall seasonal cycle in the brackish Baltic Sea surface waters, a temperate brackish water ecosystem periodically promoting massive cyanobacterial blooms, which have implications for primary production, nutrient cycling, and expansion of hypoxic zones. Network analysis of the gene expression of all microbes from 0.22 to 200 μm in size and of the major taxonomic groups dissected the seasonal cycle into four components that comprised genes peaking during different periods of the bloom. Photoautotrophic nitrogen-fixing Cyanobacteria displayed the highest connectivity among the microbes, in contrast to chemoautotrophic ammonia-oxidizing Thaumarchaeota, while heterotrophs dominated connectivity among pre- and post-bloom peaking genes. The network was also composed of distinct functional connectivities, with an early season balance between carbon metabolism and ATP synthesis shifting to a dominance of ATP synthesis during the bloom, while carbon degradation, specifically through the glyoxylate shunt, characterized the post-bloom period, driven by Alphaproteobacteria as well as by Gammaproteobacteria of the SAR86 and SAR92 clusters. Our study stresses the exceptionally strong biotic driving force executed by cyanobacterial blooms on associated microbial communities in the Baltic Sea and highlights the impact cyanobacterial blooms have on functional microbial community composition.

Effects of Hurricane-Felled Tree Trunks on Soil Carbon, Nitrogen, Microbial Biomass, and Root Length in a Wet Tropical Forest

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D. Jean Lodge

2016-11-01

Full Text Available Decaying coarse woody debris can affect the underlying soil either by augmenting nutrients that can be exploited by tree roots, or by diminishing nutrient availability through stimulation of microbial nutrient immobilization. We analyzed C, N, microbial biomass C and root length in closely paired soil samples taken under versus 20–50 cm away from large trunks of two species felled by Hugo (1989 and Georges (1998 three times during wet and dry seasons over the two years following the study conducted by Georges. Soil microbial biomass, % C and % N were significantly higher under than away from logs felled by both hurricanes (i.e., 1989 and 1998, at all sampling times and at both depths (0–10 and 10–20 cm. Frass from wood boring beetles may contribute to early effects. Root length was greater away from logs during the dry season, and under logs in the wet season. Root length was correlated with microbial biomass C, soil N and soil moisture (R = 0.36, 0.18, and 0.27, respectively; all p values < 0.05. Microbial biomass C varied significantly among seasons but differences between positions (under vs. away were only suggestive. Microbial C was correlated with soil N (R = 0.35. Surface soil on the upslope side of the logs had significantly more N and microbial biomass, likely from accumulation of leaf litter above the logs on steep slopes. We conclude that decaying wood can provide ephemeral resources that are exploited by tree roots during some seasons.

Update of Clostridium difficile infection due to PCR ribotype 027 in Europe, 2008.

LENUS (Irish Health Repository)

Kuijper, E J

2008-07-31

Outbreaks of Clostridium difficile infections (CDI) with increased severity, high relapse rate and significant mortality have been related to the emergence of a new, hypervirulent C. difficile strain in North America and Europe. This emerging strain is referred to as PCR ribotype 027 (Type 027). Since 2005, individual countries have developed surveillance studies about the spread of type 027.C. difficile Type 027 has been reported in 16 European countries. It has been responsible for outbreaks in Belgium, Germany, Finland, France, Ireland, Luxembourg, The Netherlands, Switzerland and the United Kingdom (England, Wales, Northern Ireland and Scotland). It has also been detected in Austria, Denmark, Sweden, Norway, Hungary, Poland and Spain. Three countries experienced imported patients with CDI due to Type 027 who acquired the infection abroad.The antimicrobial resistance pattern is changing, and outbreaks due to clindamycin-resistant ermB positive Type 027 strains have occurred in three European countries. Ongoing epidemiological surveillance of cases of CDI, with periodic characterisation of the strains involved, is required to detect clustering of cases in time and space and to monitor the emergence of new, highly virulent clones.

Microbial Diversity in Cerrado Biome (Neotropical Savanna Soils.

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Alinne Pereira de Castro

Full Text Available The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture.

SSU rDNA sequence diversity and seasonally differentiated distribution of nanoplanktonic ciliates in neritic Bohai and Yellow Seas as revealed by T-RFLP.

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Jun Dong

Full Text Available Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution patterns of nanoplanktonic oligotrich and choreotrich (OC ciliates in surface water of three neritic basins of northern China, the South Yellow Sea (SYS, North Yellow Sea (NYS, and Bohai Sea (BS in June and November 2011. SSU rRNA gene clone libraries generated from three summertime samples (sites B38, B4 and H8 were analyzed and revealed a large novel ribotype diversity, of which many were low-abundant phylotypes belonging to the subclass Oligotrichia, but divergent from described morphospecies. Based on the data of terminal-restriction fragment length polymorphism (T-RFLP analysis of all 35 samples, we found that the T-RF richness was generally higher in the SYS than in the BS, and negatively correlated with the molar ratio of P to Si. Overall, multidimensional scaling and permutational multivariate analysis of variance of the community turnover demonstrated a distinct seasonal pattern but no basin-to-basin differentiation across all samples. Nevertheless, significant community differences among basins were recognized in the winter dataset. Mantel tests showed that the environmental factors, P:Si ratio, water temperature and concentration of dissolved oxygen (DO, determined the community across all samples. However, both biogeographic distance and environment shaped the community in winter, with DO being the most important physicochemical factor. Our results indicate that the stoichiometric ratio of P:Si is a key factor, through which the phytoplankton community may be shaped, resulting in a cascade effect on the diversity and community composition of OC nanociliates in the N-rich, Si-limited coastal surface waters, and that the Yellow Sea Warm Current drives the nanociliate community, and possibly the

Microbial Contamination of the Food Materials for Manufacturing Korean Laver Roll (Kimbab) and the Effect of Gamma Irradiation

International Nuclear Information System (INIS)

Hong, S.P.; Kim, Y.H.; Lee, N.Y.; Jo, C.U.; Byun, M.W.

2004-01-01

Microbial contamination of ready-to-eat ingredients for Kimbab manufacturing and the effect of irradiation to reduce the microbial contamination of the products were investigated. Among 9 food items tested, there were no viable cells in the ham, seasoned and cooked beef, imitation crab leg, fried egg, and seasoned burdoc. Cucumber, surimi gel, and seasoned and blanched spinach were counted at 5.07±0.97, 3.50±0.14, and 5.41±0.51 log CFU/g, respectively

Effects of Monoculture, Crop Rotation, and Soil Moisture Content on Selected Soil Physicochemical and Microbial Parameters in Wheat Fields

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A. Marais

2012-01-01

Full Text Available Different plants are known to have different soil microbial communities associated with them. Agricultural management practices such as fertiliser and pesticide addition, crop rotation, and grazing animals can lead to different microbial communities in the associated agricultural soils. Soil dilution plates, most-probable-number (MPN, community level physiological profiling (CLPP, and buried slide technique as well as some measured soil physicochemical parameters were used to determine changes during the growing season in the ecosystem profile in wheat fields subjected to wheat monoculture or wheat in annual rotation with medic/clover pasture. Statistical analyses showed that soil moisture had an over-riding effect on seasonal fluctuations in soil physicochemical and microbial populations. While within season soil microbial activity could be differentiated between wheat fields under rotational and monoculture management, these differences were not significant.

Microbial response of an acid forest soil to experimental soil warming

Science.gov (United States)

S.S. Arnold; I.J. Fernandez; L.E. Rustad; L.M. Zibilske

1999-01-01

Effects of increased soil temperature on soil microbial biomass and dehydrogenase activity were examined on organic (O) horizon material in a low-elevation spruce-fir ecosystem. Soil temperature was maintained at 5 °C above ambient during the growing season in the experimental plots, and soil temperature, moisture, microbial biomass, and dehydrogenase activity were...

Exposure to grain dust and microbial components in the Norwegian grain and compound feed industry.

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Halstensen, Anne Straumfors; Heldal, Kari Kulvik; Wouters, Inge M; Skogstad, Marit; Ellingsen, Dag G; Eduard, Wijnand

2013-11-01

The aim of this study was to extensively characterize grain workers' personal exposure during work in Norwegian grain elevators and compound feed mills, to identify differences in exposures between the workplaces and seasons, and to study the correlations between different microbial components. Samples of airborne dust (n = 166) were collected by full-shift personal sampling during work in 20 grain elevators and compound feed mills during one autumn season and two winter seasons. The personal exposure to grain dust, endotoxins, β-1→3-glucans, bacteria, and fungal spores was quantified. Correlations between dust and microbial components and differences between workplaces and seasons were investigated. Determinants of endotoxin and β-1→3-glucan exposure were evaluated by linear mixed-effect regression modeling. The workers were exposed to an overall geometric mean of 1.0mg m(-3) inhalable grain dust [geometric standard deviation (GSD) = 3.7], 628 endotoxin units m(-3) (GSD = 5.9), 7.4 µg m(-3) of β-1→3-glucan (GSD = 5.6), 21 × 10(4) bacteria m(-3) (GSD = 7.9) and 3.6 × 10(4) fungal spores m(-3) (GSD = 3.4). The grain dust exposure levels were similar across workplaces and seasons, but the microbial content of the grain dust varied substantially between workplaces. Exposure levels of all microbial components were significantly higher in grain elevators compared with all other workplaces. The grain dust exposure was significantly correlated (Pearson's r) with endotoxin (rp = 0.65), β-1→3-glucan (rp = 0.72), bacteria (rp = 0.44) and fungal spore (rp = 0.48) exposure, whereas the explained variances were strongly dependent on the workplace. Bacteria, grain dust, and workplace were important determinants for endotoxin exposure, whereas fungal spores, grain dust, and workplace were important determinants for β-1→3-glucan exposure. Although the workers were exposed to a relatively low mean dust level, the microbial exposure was high. Furthermore, the

Effect of storage time on microbial quality of some spices and dried ...

African Journals Online (AJOL)

The effect of storage time on the microbial quality of some spices and dried seasonings (SDS) (dawadawa, pepper, ginger, shrimp and fish powders) was studied over a 12-month period. Microbial load and profile of irradiated and unirradiated SDS were assessed at 0, 6 and 12-month periods. The range of total variable ...

Monitoring Seasonal Changes in Winery-Resident Microbiota.

Science.gov (United States)

Bokulich, Nicholas A; Ohta, Moe; Richardson, Paul M; Mills, David A

2013-01-01

During the transformation of grapes to wine, wine fermentations are exposed to a large area of specialized equipment surfaces within wineries, which may serve as important reservoirs for two-way transfer of microbes between fermentations. However, the role of winery environments in shaping the microbiota of wine fermentations and vectoring wine spoilage organisms is poorly understood at the systems level. Microbial communities inhabiting all major equipment and surfaces in a pilot-scale winery were surveyed over the course of a single harvest to track the appearance of equipment microbiota before, during, and after grape harvest. Results demonstrate that under normal cleaning conditions winery surfaces harbor seasonally fluctuating populations of bacteria and fungi. Surface microbial communities were dependent on the production context at each site, shaped by technological practices, processing stage, and season. During harvest, grape- and fermentation-associated organisms populated most winery surfaces, acting as potential reservoirs for microbial transfer between fermentations. These surfaces harbored large populations of Saccharomyces cerevisiae and other yeasts prior to harvest, potentially serving as an important vector of these yeasts in wine fermentations. However, the majority of the surface communities before and after harvest comprised organisms with no known link to wine fermentations and a near-absence of spoilage-related organisms, suggesting that winery surfaces do not overtly vector wine spoilage microbes under normal operating conditions.

Monitoring Seasonal Changes in Winery-Resident Microbiota.

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Nicholas A Bokulich

Full Text Available During the transformation of grapes to wine, wine fermentations are exposed to a large area of specialized equipment surfaces within wineries, which may serve as important reservoirs for two-way transfer of microbes between fermentations. However, the role of winery environments in shaping the microbiota of wine fermentations and vectoring wine spoilage organisms is poorly understood at the systems level. Microbial communities inhabiting all major equipment and surfaces in a pilot-scale winery were surveyed over the course of a single harvest to track the appearance of equipment microbiota before, during, and after grape harvest. Results demonstrate that under normal cleaning conditions winery surfaces harbor seasonally fluctuating populations of bacteria and fungi. Surface microbial communities were dependent on the production context at each site, shaped by technological practices, processing stage, and season. During harvest, grape- and fermentation-associated organisms populated most winery surfaces, acting as potential reservoirs for microbial transfer between fermentations. These surfaces harbored large populations of Saccharomyces cerevisiae and other yeasts prior to harvest, potentially serving as an important vector of these yeasts in wine fermentations. However, the majority of the surface communities before and after harvest comprised organisms with no known link to wine fermentations and a near-absence of spoilage-related organisms, suggesting that winery surfaces do not overtly vector wine spoilage microbes under normal operating conditions.

Seasonal Variations in Sugar Contents and Microbial Community Behavior in a Ryegrass Soil

Science.gov (United States)

Medeiros, P. M.; Fernandes, M. F.; Dick, R. P.; Simoneit, B. R.

2004-12-01

Soil is a complex mixture of numerous inorganic and organic constituents that vary in size, shape, chemical constitution and reactivity, and hosts numerous organisms. Total sugars have been estimated to constitute 10% (average) of soil organic matter, occurring in living and decaying organisms, as well as in extracellular materials. The role of sugars in soils is attributed to their influence on soil structure, chemical processes, plant nutrition and microbial activity. The sources of sugars in soils are: a) plants (the primary source); b) animals (the minor source), and c) microorganisms (fungi, bacteria, algae), which decompose the primary plant and animal material, and synthesize the major part of soil carbohydrates. A particular soil sample provides a momentary glimpse into a dynamic system (continuous addition, degradation and synthesis) that might, except for seasonal variations, be in equilibrium. The purpose of this study is to identify and quantify the major sugars in a grass soil and characterize the relationship between their concentration variations and soil microbial behavior over an annual cycle. Soil samples were collected monthly in a ryegrass field close to Corvallis, Oregon, and analyzed by gas chromatography-mass spectrometry as total silylated extracts for sugar composition, and by gas chromatography-flame ionization as fatty acid methyl esters derived from phospholipids and neutral lipids (PLFA and NLFA, respectively). The preliminary results of the first six-month experiment (from January to June, 2004) show that as the ambient temperatures increase the sugar concentrations (glucose, fructose, sucrose and trehalose) also tend to increase in the soil. A decrease is observed in March when precipitation was low during the whole month. The same trend is observed for the active biomass of fungi and bacteria estimated by their fatty acids derived from phospholipids. Fatty acids 18:2ω 6c and 18:3ω 6c are used as fungal biomarkers. Branched (15:0i

Microbial population changes in tropical agricultural soil ...

African Journals Online (AJOL)

Impacts of crude petroleum pollution on the soil environment and microbial population dynamics as well as recovery rates of an abandoned farmland was monitored for seven months spanning the two major seasons in Nigeria with a ... The physico-chemistry of the control and contaminated soils differed just significantly (P ...

Single Cell Analysis Linking Ribosomal (r)DNA and rRNA Copy Numbers to Cell Size and Growth Rate Provides Insights into Molecular Protistan Ecology.

Science.gov (United States)

Fu, Rao; Gong, Jun

2017-11-01

Ribosomal (r)RNA and rDNA have been golden molecular markers in microbial ecology. However, it remains poorly understood how ribotype copy number (CN)-based characteristics are linked with diversity, abundance, and activity of protist populations and communities observed at organismal levels. Here, we applied a single-cell approach to quantify ribotype CNs in two ciliate species reared at different temperatures. We found that in actively growing cells, the per-cell rDNA and rRNA CNs scaled with cell volume (CV) to 0.44 and 0.58 powers, respectively. The modeled rDNA and rRNA concentrations thus appear to be much higher in smaller than in larger cells. The observed rRNA:rDNA ratio scaled with CV 0.14 . The maximum growth rate could be well predicted by a combination of per-cell ribotype CN and temperature. Our empirical data and modeling on single-cell ribotype scaling are in agreement with both the metabolic theory of ecology and the growth rate hypothesis, providing a quantitative framework for linking cellular rDNA and rRNA CNs with body size, growth (activity), and biomass stoichiometry. This study also demonstrates that the expression rate of rRNA genes is constrained by cell size, and favors biomass rather than abundance-based interpretation of quantitative ribotype data in population and community ecology of protists. © 2017 The Authors. Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

Glyphosate toxicity and the effects of long-term vegetation control on soil microbial communities

Science.gov (United States)

Matt D. Busse; Alice W. Ratcliff; Carol J. Stestak; Robert F. Powers

2001-01-01

We assessed the direct and indirect effect of the herbicide glyphosate on soil microbial communities from soil bioassays at glyphosate concentrations up to 100-fold greater than expected following a single field application. Indirect effects on microbial biomass, respiration, and metabolic diversity (Biolog and catabolic response profile) were compared seasonally after...

Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

Science.gov (United States)

He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

2014-12-01

Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

Potential microbial risk factors related to soil amendments and irrigation water of potato crops.

Science.gov (United States)

Selma, M V; Allende, A; López-Gálvez, F; Elizaquível, P; Aznar, R; Gil, M I

2007-12-01

This study assesses the potential microbial risk factors related to the use of soil amendments and irrigation water on potato crops, cultivated in one traditional and two intensive farms during two harvest seasons. The natural microbiota and potentially pathogenic micro-organisms were evaluated in the soil amendment, irrigation water, soil and produce. Uncomposted amendments and residual and creek water samples showed the highest microbial counts. The microbial load of potatoes harvested in spring was similar among the tested farms despite the diverse microbial levels of Listeria spp. and faecal coliforms in the potential risk sources. However, differences in total coliform load of potato were found between farms cultivated in the autumn. Immunochromatographic rapid tests and the BAM's reference method (Bacteriological Analytical Manual; AOAC International) were used to detect Escherichia coli O157:H7 from the potential risk sources and produce. Confirmation of the positive results by polymerase chain reaction procedures showed that the immunochromatographic assay was not reliable as it led to false-positive results. The potentially pathogenic micro-organisms of soil amendment, irrigation water and soil samples changed with the harvest seasons and the use of different agricultural practices. However, the microbial load of the produce was not always influenced by these risk sources. Improvements in environmental sample preparation are needed to avoid interferences in the use of immunochromatographic rapid tests. The potential microbial risk sources of fresh produce should be regularly controlled using reliable detection methods to guarantee their microbial safety.

Microbial water quality of coastal recreational water in the Gaza Strip, Palestine

Directory of Open Access Journals (Sweden)

MAZEN T. ABUALTAYEF

2014-05-01

Full Text Available Abualtayef MT, Abd Rabou AN, Abu Foul AA, Ghabayen SM, Elsinwar HM. 2014. Microbial water quality of coastal recreational water in the Gaza Strip, Palestine. Nusantara Bioscience 6: 26-32. Wastewater disposal into the Mediterranean coast of the Gaza Strip has many negative effects, whether on the environment or on human health, thus microbiological analysis of seawater samples was carried out. The microbial analysis was confined on two types of fecal indicators (fecal coliform and fecal streptococci, in addition to a single type of bacteria (pseudomonas. This study was conducted between the beginning of July 2012 to the mid of October 2012 over an area extended from the proposed Khan Younis fishing port to Gaza fishing port, with a length of about 23 km. The study area was divided into five zones. The samples were collected in two rounds: the first round included 75 samples that collected along the study area during the summer season. The second round included 19 samples that collected in the autumn season to compare it with their counterparts that have been collected in the summer season. Laboratory analysis showed the presence of contamination in many of these samples. The results also showed that the pollution was concentrated in and surrounding the mouths of wastewater outfalls. Depending on the microbial analyses, which have been collected in the first round, the fecal coliform appeared in 61% of the samples, while fecal streptococci appeared in all samples and pseudomonas appeared in 33% of the samples. The pollutants were widespread along the study area, which are the result mainly from wastewater discharge into the sea. A risk analysis was done for season variations using the second moment method; in general, it was found that risk in both seasons was high especially in summer.

Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression

OpenAIRE

Har, Jia Y.; Helbig, Tim; Lim, Ju H.; Fernando, Samodha C.; Reitzel, Adam M.; Penn, Kevin; Thompson, Janelle R.

2015-01-01

We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacter...

Marine heatwaves and optimal temperatures for microbial assemblage activity

OpenAIRE

Joint, IR; Smale, DA

2016-01-01

The response of microbial assemblages to instantaneous temperature change was measured in a seasonal study of the coastal waters of the western English Channel. On 18 occasions between November 1999 and December 2000, bacterial abundance was assessed and temperature responses determined from the incorporation of 3H leucine, measured in a temperature gradient from 5°C to 38°C. Q10 values varied, being close to 2 in spring and summer but were >3 in autumn. There was a seasonal pattern in the as...

Termites and flooding affect microbial communities in decomposing wood

Science.gov (United States)

Michael D. Ulyshen; Susan V. Diehl; Dragica Jeremic

2016-01-01

Wood properties and microbial community characteristics were compared between loblolly pine (Pinus taeda L.) logs protected or unprotected from termites (Blattodea: Rhinotermitidae: Reticulitermes spp.) and other arthropods for two years in seasonally flooded and unflooded forests in the southeastern United States. Significant compositional differences were observed...

Soil Biogeochemical and Microbial Feedbacks along a Snowmelt-Dominated Hillslope-to-Floodplain Transect in Colorado.

Science.gov (United States)

Sorensen, P.; Beller, H. R.; Bill, M.; Bouskill, N.; Brodie, E.; Chakraborty, R.; Conrad, M. E.; Karaoz, U.; Polussa, A.; Steltzer, H.; Wang, S.; Williams, K. H.; Wilmer, C.; Wu, Y.

2017-12-01

Nitrogen export from mountainous watersheds is a product of multiple interactions among hydrological processes and soil-microbial-plant feedbacks along the continuum from terrestrial to aquatic environments. In snow-dominated systems, like the East River Watershed (CO), seasonal processes such as snowmelt exert significant influence on the annual hydrologic cycle and may also link spatially distinct catchment subsystems, such as hillslope and adjoining riparian floodplains. Further, snowmelt is occurring earlier each year and this is predicted to result in a temporal asynchrony between historically coupled microbial nutrient release and plant nutrient demand in spring, with the potential to increase N export from the East River Watershed. Here we summarize biogeochemical data collected along a hillslope-to-riparian floodplain transect at the East River site. Starting in Fall 2016, we sampled soils at 3 depths and measured dissolved pools of soil nutrients (e.g., NH4+, NO3-, DOC, P), microbial biomass CN, and microbial community composition over a seasonal time course, through periods of snow accumulation, snowmelt, and plant senescence. Soil moisture content in the top 5 cm of floodplain soils was nearly 4X greater across sampling dates, coinciding with 2X greater microbial biomass C, larger extractable pools of NH4+, and smaller pools of NO3- in floodplain vs. hillslope soils. These results suggest that microbially mediated redox processes played an important role in N cycling along the transect. Hillslope vs. floodplain location also appeared to be a key factor that differentiated soil microbial communities (e.g., a more important factor than seasonality or soil depth or type). Snow accumulation and snowmelt exerted substantial influence on soil biogeochemistry. For example, microbial biomass accumulation increased about 2X beneath the winter snowpack. Snowmelt resulted in a precipitous crash in the microbial population, with 2.5X reductions in floodplain and 2X

Marked seasonal variation in the wild mouse gut microbiota.

Science.gov (United States)

Maurice, Corinne F; Knowles, Sarah C L; Ladau, Joshua; Pollard, Katherine S; Fenton, Andy; Pedersen, Amy B; Turnbaugh, Peter J

2015-11-01

Recent studies have provided an unprecedented view of the microbial communities colonizing captive mice; yet the host and environmental factors that shape the rodent gut microbiota in their natural habitat remain largely unexplored. Here, we present results from a 2-year 16 S ribosomal RNA gene sequencing-based survey of wild wood mice (Apodemus sylvaticus) in two nearby woodlands. Similar to other mammals, wild mice were colonized by 10 bacterial phyla and dominated by the Firmicutes, Bacteroidetes and Proteobacteria. Within the Firmicutes, the Lactobacillus genus was most abundant. Putative bacterial pathogens were widespread and often abundant members of the wild mouse gut microbiota. Among a suite of extrinsic (environmental) and intrinsic (host-related) factors examined, seasonal changes dominated in driving qualitative and quantitative differences in the gut microbiota. In both years examined, we observed a strong seasonal shift in gut microbial community structure, potentially due to the transition from an insect- to a seed-based diet. This involved decreased levels of Lactobacillus, and increased levels of Alistipes (Bacteroidetes phylum) and Helicobacter. We also detected more subtle but statistically significant associations between the gut microbiota and biogeography, sex, reproductive status and co-colonization with enteric nematodes. These results suggest that environmental factors have a major role in shaping temporal variations in microbial community structure within natural populations.

Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels.

Science.gov (United States)

Ren, Tiantian; Boutin, Stan; Humphries, Murray M; Dantzer, Ben; Gorrell, Jamieson C; Coltman, David W; McAdam, Andrew G; Wu, Martin

2017-12-21

Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducted a comprehensive study of gut microbiota of a well-studied North American red squirrel (Tamiasciurus hudsonicus) population. Red squirrels are territorial, solitary, and live in a highly seasonal environment and therefore represent a very attractive system to study factors that drive the temporal and spatial dynamics of gut microbiota. For the first time, this study revealed significant spatial patterns of gut microbiota within a host population, suggesting limited dispersal could play a role in shaping and maintaining the structure of gut microbial communities. We also found a remarkable seasonal rhythm in red squirrel's gut microbial composition manifested by a tradeoff between relative abundance of two genera Oscillospira and Corpococcus and clearly associated with seasonal variation in diet availability. Our results show that in nature, environmental factors exert a much stronger influence on gut microbiota than host-associated factors including age and sex. Despite strong environmental effects, we found clear evidence of individuality and maternal effects, but host genetics did not seem to be a significant driver of the gut microbial communities in red squirrels. Taken together, the results of this study emphasize the importance of external ecological factors rather than host attributes in driving temporal and spatial patterns of gut microbiota in natural environment.

Effects of Seasonal and Perennial Grazing on Soil Fauna Community and Microbial Biomass Carbon in the Subalpine Meadows of Yunnan, Southwest China

Institute of Scientific and Technical Information of China (English)

LIU Shengjie; YANG Xiaodong; Anthony R.IVES; FENG Zhili; SHA Liqing

2017-01-01

Grazing and over-grazing may drive changes in the diversity and functioning of below-ground meadow ecosystems.A field soil survey was conducted to compare microbial biomass carbon (Cmin) and soil fauna communities in the two main grassland management systems in subalpine regions of Yunnan Province,China:perennial grazing currently practiced due to increasing herd sizes and traditional seasonal grazing.A three-year exclosure experiment was then conducted to further compare the effects of different grazing practices,including treatments of no mowing,perennial grazing (NM + G),mowing followed by seasonal grazing (M + G),mowing and no grazing (M + NG),and no mowing or grazing (NM + NG).The comparative survey result revealed that Cmin and total density of soil fauna were significantly lower at a perennially grazed site than at a seasonally grazed site.The experiment results showed that in comparison to non-grazing treatments (M + NG and NM + NG),grazing (NM + G and M + G) reduced total fauna density (by 150 individuals m-2) and the number of taxonomic groups present (by 0.32 taxa m-2).Mowing decreased Cmin (by 0.31 mg g-1).Furthermore,the NM + G treatment (perennial grazing) had the lowest density of Collembola (16.24 individuals m-2),one of the two most common taxonomic groups,although other taxonomic groups responded differently to the treatments.Treatment effects on soil fauna were consistent with those on above-ground grasses,in which C:N ratios were greatly reduced by grazing,with this effect being the greatest for the NM + G treatment.In contrast,different grazing treatments had little effect on C:N ratio of soil.Furthermore,the traditional grazing method (mowing followed by seasonal grazing) may have less severe effects on some taxonomic groups than perennial grazing.Therefore,an appropriate management should aim to protect soil fauna and microbes in this area from over-grazing and against further degradation.

Biochemical properties and microbial analysis of honey from North ...

African Journals Online (AJOL)

In the present study, physicochemical properties (pH, ash, commercial glucose, starch, reducing sugars and moisture) and microbial (yeast and enterobacterial) contaminations of 263 honey samples from North-western regions of Iran were evaluated in a 2 year period in different seasons of 2010 and 2011. Levels of ...

Effects of Biochar on Soil Microbial Biomass after Four Years of Consecutive Application in the North China Plain

Science.gov (United States)

Zhang, Qing-zhong; Dijkstra, Feike A.; Liu, Xing-ren; Wang, Yi-ding; Huang, Jian; Lu, Ning

2014-01-01

The long term effect of biochar application on soil microbial biomass is not well understood. We measured soil microbial biomass carbon (MBC) and nitrogen (MBN) in a field experiment during a winter wheat growing season after four consecutive years of no (CK), 4.5 (B4.5) and 9.0 t biochar ha−1 yr−1 (B9.0) applied. For comparison, a treatment with wheat straw residue incorporation (SR) was also included. Results showed that biochar application increased soil MBC significantly compared to the CK treatment, and that the effect size increased with biochar application rate. The B9.0 treatment showed the same effect on MBC as the SR treatment. Treatments effects on soil MBN were less strong than for MBC. The microbial biomass C∶N ratio was significantly increased by biochar. Biochar might decrease the fraction of biomass N mineralized (K N), which would make the soil MBN for biochar treatments underestimated, and microbial biomass C∶N ratios overestimated. Seasonal fluctuation in MBC was less for biochar amended soils than for CK and SR treatments, suggesting that biochar induced a less extreme environment for microorganisms throughout the season. There was a significant positive correlation between MBC and soil water content (SWC), but there was no significant correlation between MBC and soil temperature. Biochar amendments may therefore reduce temporal variability in environmental conditions for microbial growth in this system thereby reducing temporal fluctuations in C and N dynamics. PMID:25025330

Effects of biochar on soil microbial biomass after four years of consecutive application in the north China Plain.

Directory of Open Access Journals (Sweden)

Qing-zhong Zhang

Full Text Available The long term effect of biochar application on soil microbial biomass is not well understood. We measured soil microbial biomass carbon (MBC and nitrogen (MBN in a field experiment during a winter wheat growing season after four consecutive years of no (CK, 4.5 (B4.5 and 9.0 t biochar ha(-1 yr(-1 (B9.0 applied. For comparison, a treatment with wheat straw residue incorporation (SR was also included. Results showed that biochar application increased soil MBC significantly compared to the CK treatment, and that the effect size increased with biochar application rate. The B9.0 treatment showed the same effect on MBC as the SR treatment. Treatments effects on soil MBN were less strong than for MBC. The microbial biomass C∶N ratio was significantly increased by biochar. Biochar might decrease the fraction of biomass N mineralized (KN, which would make the soil MBN for biochar treatments underestimated, and microbial biomass C∶N ratios overestimated. Seasonal fluctuation in MBC was less for biochar amended soils than for CK and SR treatments, suggesting that biochar induced a less extreme environment for microorganisms throughout the season. There was a significant positive correlation between MBC and soil water content (SWC, but there was no significant correlation between MBC and soil temperature. Biochar amendments may therefore reduce temporal variability in environmental conditions for microbial growth in this system thereby reducing temporal fluctuations in C and N dynamics.

The Microbiome Structure of Oklahoma Cropland and Prairie Soils and its Response to Seasonal Forcing and Management Practices

Science.gov (United States)

Cornell, C. R.; Peterson, B.; Zhou, J.; Xiao, X.; Wawrik, B.

2017-12-01

Greenhouse gases (GHG) emissions from soils are primarily the consequence of microbial processes. Agricultural management of soils is known to affect the structure of microbial communities, and it is likely that dominant GHG emitting microbial activities are impacted via requisite practices. To gain better insight into the impact of seasonal forcing and management practices on the microbiome structure in Oklahoma agricultural soils, a seasonal study was conducted. Over a year period, samples were collected bi-weekly during wet months, and monthly during dry months from two grassland and two managed agricultural sites in El Reno, Oklahoma. Microbial community structure was determined in quadruplicate for each site and time point via 16S rRNA gene sequencing. Measures of soil water content, subsoil nitrate, ammonium, organic matter, total nitrogen, and biomass were also taken for each time point. Data analysis revealed several important trends, indicating greater microbial diversity in native grassland and distinct microbial community changes in response to management practices. The native grassland soils also contained greater microbial biomass than managed soils and both varied in response to rainfall events. Native grassland soils harbor more diverse microbial communities, with the diversity and biomass decreasing along a gradient of agricultural management intensity. These data indicate that microbial community structure in El Reno soils occurs along a continuum in which native grasslands and highly managed agricultural soils (tilling and manure application) form end members. Integration with measurements from eddy flux towers into modelling efforts using the DeNitrification-DeComposition (DNDC) model is currently being explored to improve predictions of GHG emissions from grassland soils.

Microbial activity, arbuscular mycorrhizal fungi and inoculation of woody plants in lead contaminated soil

Directory of Open Access Journals (Sweden)

Graziella S Gattai

2011-09-01

Full Text Available The goals of this study were to evaluate the microbial activity, arbuscular mycorrhizal fungi and inoculation of woody plants (Caesalpinia ferrea, Mimosa tenuiflora and Erythrina velutina in lead contaminated soil from the semi-arid region of northeastern of Brazil (Belo Jardim, Pernambuco. Dilutions were prepared by adding lead contaminated soil (270 mg Kg-1 to uncontaminated soil (37 mg Pb Kg soil-1 in the proportions of 7.5%, 15%, and 30% (v:v. The increase of lead contamination in the soil negatively influenced the amount of carbon in the microbial biomass of the samples from both the dry and rainy seasons and the metabolic quotient only differed between the collection seasons in the 30% contaminated soil. The average value of the acid phosphatase activity in the dry season was 2.3 times higher than observed during the rainy season. There was no significant difference in the number of glomerospores observed between soils and periods studied. The most probable number of infective propagules was reduced for both seasons due to the excess lead in soil. The mycorrhizal colonization rate was reduced for the three plant species assayed. The inoculation with arbuscular mycorrhizal fungi benefited the growth of Erythrina velutina in lead contaminated soil.

Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay.

Science.gov (United States)

Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Zheng, Wei; Wen, Donghui

2016-06-01

Anthropogenic activities usually contaminate water environments, and have led to the eutrophication of many estuaries and shifts in microbial communities. In this study, the temporal and spatial changes of the microbial community in an industrial effluent receiving area in Hangzhou Bay were investigated by 454 pyrosequencing. The bacterial community showed higher richness and biodiversity than the archaeal community in all sediments. Proteobacteria dominated in the bacterial communities of all the samples; Marine_Group_I and Methanomicrobia were the two dominant archaeal classes in the effluent receiving area. PCoA and AMOVA revealed strong seasonal but minor spatial changes in both bacterial and archaeal communities in the sediments. The seasonal changes of the bacterial community were less significant than those of the archaeal community, which mainly consisted of fluctuations in abundance of a large proportion of longstanding species rather than the appearance and disappearance of major archaeal species. Temperature was found to positively correlate with the dominant bacteria, Betaproteobacteria, and negatively correlate with the dominant archaea, Marine_Group_I; and might be the primary driving force for the seasonal variation of the microbial community. Copyright © 2016. Published by Elsevier B.V.

Thermal barriers constrain microbial elevational range size via climate variability.

Science.gov (United States)

Wang, Jianjun; Soininen, Janne

2017-08-01

Range size is invariably limited and understanding range size variation is an important objective in ecology. However, microbial range size across geographical gradients remains understudied, especially on mountainsides. Here, the patterns of range size of stream microbes (i.e., bacteria and diatoms) and macroorganisms (i.e., macroinvertebrates) along elevational gradients in Asia and Europe were examined. In bacteria, elevational range size showed non-significant phylogenetic signals. In all taxa, there was a positive relationship between niche breadth and species elevational range size, driven by local environmental and climatic variables. No taxa followed the elevational Rapoport's rule. Climate variability explained the most variation in microbial mean elevational range size, whereas local environmental variables were more important for macroinvertebrates. Seasonal and annual climate variation showed negative effects, while daily climate variation had positive effects on community mean elevational range size for all taxa. The negative correlation between range size and species richness suggests that understanding the drivers of range is key for revealing the processes underlying diversity. The results advance the understanding of microbial species thermal barriers by revealing the importance of seasonal and diurnal climate variation, and highlight that aquatic and terrestrial biota may differ in their response to short- and long-term climate variability. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Perspectives of microbial oils for biodiesel production

Energy Technology Data Exchange (ETDEWEB)

Li Qiang; Du Wei; Liu Dehua [Tsinghua Univ., Beijing (China). Dept. of Chemical Engineering

2008-10-15

Biodiesel has become more attractive recently because of its environmental benefits, and the fact that it is made from renewable resources. Generally speaking, biodiesel is prepared through transesterification of vegetable oils or animal fats with short chain alcohols. However, the lack of oil feedstocks limits the large-scale development of biodiesel to some extent. Recently, much attention has been paid to the development of microbial, oils and it has been found that many microorganisms, such as algae, yeast, bacteria, and fungi, have the ability to accumulate oils under some special cultivation conditions. Compared to other plant oils, microbial oils have many advantages, such as short life cycle, less labor required, less affection by venue, season and climate, and easier to scale up. With the rapid expansion of biodiesel, microbial oils might become one of potential oil feedstocks for biodiesel production in the future, though there are many works associated with microorganisms producing oils need to be carried out further. This review is covering the related research about different oleaginous microorganisms producing oils, and the prospects of such microbial oils used for biodiesel production are also discussed. (orig.)

Characterization of Escherichia coli populations from gulls, landfill trash, and wastewater using ribotyping.

Science.gov (United States)

Nelson, M; Jones, S H; Edwards, C; Ellis, J C

2008-08-19

Due to their opportunistic and gregarious nature, gulls may be important reservoirs and vectors for anthropogenically derived fecal pathogens in coastal areas. We used ribotyping, a genotypic bacterial source tracking method, to compare populations of Escherichia coli among herring gulls Larus argentatus, great black-backed gulls L. marinus, wastewater, and landfill trash in New Hampshire and Maine, USA. Concentrations of E. coli in gull feces varied widely among individuals, but were generally high (6.0 x 10(1) to 2.5 x 10(9) g(-1) wet weight). Of 39 E. coli isolates from L. argentatus, 67% had banding patterns that were > or = 90% similar to those from wastewater and trash, whereas only 39% of 36 L. marinus isolates exhibited > or = 90% similarity to these sources. Strains of E. coli from gulls matched (> or = 90% similarity) more strains from wastewater (39% matching) than from trash (15% matching). E. coli isolates from L. marinus feces exhibited a greater diversity of banding patterns than did isolates from L. argentatus. There were more unique E. coli banding patterns in trash samples than in wastewater, and higher diversity indices in the former compared to the latter. These findings suggest that both species of gulls, especially L. argentatus, obtain fecal bacteria from wastewater and landfill trash, which they may transport to recreational beaches and waters. Our results also indicate that E. coli populations may vary widely between gull species, and between the anthropogenic habitats that they frequent, i.e. landfills and wastewater treatment facilities.

Seasonal Belowground Ecosystem and Eco-enzymatic Responses to Soil pH and Phosphorus Availability in Temperate Hardwood Forests

Science.gov (United States)

Smemo, K. A.; Deforest, J. L.; Petersen, S. L.; Burke, D.; Hewins, C.; Kluber, L. A.; Kyker, S. R.

2013-12-01

Atmospheric acid deposition can increase phosphorus (P) limitation in temperate hardwood forests by increasing N availability, and therefore P demand, and/or by decreasing pH and occluding inorganic P. However, only recently have studies demonstrated that P limitation can occur in temperate forests and very little is known about the temporal aspects of P dynamics in acidic forest soils and how seasonal shifts in nutrient availability and demand influence microbial investment in extracellular enzymes. The objectives of this study were to investigate how P availability and soil pH influence seasonal patterns of nutrient cycling and soil microbial activity in hardwood forests that experience chronic acid deposition. We experimentally manipulated soil pH, P, or both for three years and examined soil treatment responses in fall, winter, spring, early summer, and late summer. We found that site (glaciated versus unglaciated) and treatment had the most significant influence on nutrient pools and cycling. In general, nutrient pools were higher in glaciated soils than unglaciated for measured nutrients, including total C and N (2-3 times higher), extractable inorganic nitrogen, and readily available P. Treatment had no impact on total C and N pools in either region, but did affect other measured nutrients such as ammonium, which was greatest in the elevated pH treatment for both sites. As expected, readily available P pools were highest in the elevated P treatments (3 fold increase in both sites), but raising pH decreased available P pools in the glaciated site. Raising soil pH increased both net N mineralization rates and net P mineralization rates, regardless of site. Nitrification responses were complex, but we observed an overall significant nitrification increase under elevated pH, particularly in the growing season. Extracellular enzyme activity showed more seasonal patterns than site and treatment effects, exhibiting significant growing season activity reductions for

Estimation of microbial protein supply of lactating dairy cows under smallholder farms in north-east Thailand using urinary purine derivative technique

International Nuclear Information System (INIS)

Pimpa, O.; Liang, J.B.

2004-01-01

Two experiments were conducted to examine the potential of urinary purine derivative (PD) as a predictive index of microbial protein supply in ruminant livestock under farm conditions. Results of Experiment 1 indicated that diurnal variation in the PDC index ( [mmol/L PD]/[mmol/L creatinine] kgW 0.75 ) in spot urine samples of zebu cattle was small and highly correlated with the daily PD output, suggesting that spot urine samples could be used to derive an index for estimating microbial protein supply of cattle under farm conditions. However, the PDC index for buffaloes was poorly correlated to daily urinary PD output, therefore the use of spot urine samples appeared to be unsuitable for buffaloes. Based on the above results, spot urine samples were used to estimate the microbial protein supply of lactating dairy cows under farm conditions in a follow-up experiment. The study was conducted using 24 lactating cows in 6 smallholder dairy farms situated in Khon Kaen province of Northeast Thailand. The study was conducted over two climatic seasons (raining and dry), where the animals were fed 5 kg of farm-mixed concentrate feed supplemented either with green grass (cut or grazing) or rice straw as roughage source during the raining and dry seasons, respectively. The results indicated that microbial protein supply was not significantly different and therefore, the nutritional status of the lactating cows was not significantly different between the two seasons. The absence of differences in milk yield between seasons seems to support our findings. We conclude that urinary PD technique could be used to estimate rumen microbial protein production for dairy cattle under farm conditions. (author)

Soil microbial community profiles and functional diversity in limestone cedar glades

Science.gov (United States)

Cartwright, Jennifer M.; Dzantor, E. Kudjo; Momen, Bahram

2016-01-01

Rock outcrop ecosystems, such as limestone cedar glades (LCGs), are known for their rare and endemic plant species adapted to high levels of abiotic stress. Soils in LCGs are thin (< 25 cm), soil-moisture conditions fluctuate seasonally between xeric and saturated, and summer soil temperatures commonly exceed 48 °C. The effects of these stressors on soil microbial communities (SMC) remain largely unstudied, despite the importance of SMC-plant interactions in regulating the structure and function of terrestrial ecosystems. SMC profiles and functional diversity were characterized in LCGs using community level physiological profiling (CLPP) and plate-dilution frequency assays (PDFA). Most-probable number (MPN) estimates and microbial substrate-utilization diversity (H) were positively related to soil thickness, soil organic matter (OM), soil water content, and vegetation density, and were diminished in alkaline soil relative to circumneutral soil. Soil nitrate showed no relationship to SMCs, suggesting lack of N-limitation. Canonical correlation analysis indicated strong correlations between microbial CLPP patterns and several physical and chemical properties of soil, primarily temperature at the ground surface and at 4-cm depth, and secondarily soil-water content, enabling differentiation by season. Thus, it was demonstrated that several well-described abiotic determinants of plant community structure in this ecosystem are also reflected in SMC profiles.

Impact of seasonal variation on Escherichia coli concentrations in the riverbed sediments in the Apies River, South Africa.

Science.gov (United States)

Abia, Akebe Luther King; Ubomba-Jaswa, Eunice; Momba, Maggy Ndombo Benteke

2015-12-15

Many South Africans living in resource-poor settings with little or no access to pipe-borne water still rely on rivers as alternative water sources for drinking and other purposes. The poor microbial quality of such water bodies calls for appropriate monitoring. However, routine monitoring only takes into consideration the microbial quality of the water column, and does not include monitoring of the riverbed sediments for microbial pollution. This study sought to investigate the microbial quality of riverbed sediments in the Apies River, Gauteng Province, South Africa, using Escherichia coli as a faecal indicator organism and to investigate the impact of seasonal variation on its abundance. Weekly samples were collected at 10 sampling sites on the Apies River between May and August 2013 (dry season) and between January and February 2014 (wet season). E. coli was enumerated using the Colilert®-18 Quanti-Tray® 2000 system. All sites tested positive for E. coli. Wastewater treatment work effluents had the highest negative impact on the river water quality. Seasonal variations had an impact on the concentration of E. coli both in water and sediments with concentrations increasing during the wet season. A strong positive correlation was observed between temperature and the E. coli concentrations. We therefore conclude that the sediments of the Apies River are heavily polluted with faecal indicator bacteria and could also harbour other microorganisms including pathogens. The release of such pathogens into the water column as a result of the resuspension of sediments due to extreme events like floods or human activities could increase the health risk of the populations using the untreated river water for recreation and other household purposes. There is therefore an urgent need to reconsider and review the current South African guidelines for water quality monitoring to include sediments, so as to protect human health and other aquatic lives. Copyright © 2015 Elsevier

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris.

Science.gov (United States)

Oberbeckmann, Sonja; Osborn, A Mark; Duhaime, Melissa B

2016-01-01

Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris

Science.gov (United States)

Osborn, A. Mark

2016-01-01

Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5–6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae—all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris.

Directory of Open Access Journals (Sweden)

Sonja Oberbeckmann

Full Text Available Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate (PET drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates and diatoms (e.g. Coscinodiscophytina, Bacillariophytina. The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

Directory of Open Access Journals (Sweden)

Cody Springer Sheik

2015-05-01

Full Text Available Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time.

CMEIAS color segmentation: an improved computing technology to process color images for quantitative microbial ecology studies at single-cell resolution.

Science.gov (United States)

Gross, Colin A; Reddy, Chandan K; Dazzo, Frank B

2010-02-01

Quantitative microscopy and digital image analysis are underutilized in microbial ecology largely because of the laborious task to segment foreground object pixels from background, especially in complex color micrographs of environmental samples. In this paper, we describe an improved computing technology developed to alleviate this limitation. The system's uniqueness is its ability to edit digital images accurately when presented with the difficult yet commonplace challenge of removing background pixels whose three-dimensional color space overlaps the range that defines foreground objects. Image segmentation is accomplished by utilizing algorithms that address color and spatial relationships of user-selected foreground object pixels. Performance of the color segmentation algorithm evaluated on 26 complex micrographs at single pixel resolution had an overall pixel classification accuracy of 99+%. Several applications illustrate how this improved computing technology can successfully resolve numerous challenges of complex color segmentation in order to produce images from which quantitative information can be accurately extracted, thereby gain new perspectives on the in situ ecology of microorganisms. Examples include improvements in the quantitative analysis of (1) microbial abundance and phylotype diversity of single cells classified by their discriminating color within heterogeneous communities, (2) cell viability, (3) spatial relationships and intensity of bacterial gene expression involved in cellular communication between individual cells within rhizoplane biofilms, and (4) biofilm ecophysiology based on ribotype-differentiated radioactive substrate utilization. The stand-alone executable file plus user manual and tutorial images for this color segmentation computing application are freely available at http://cme.msu.edu/cmeias/ . This improved computing technology opens new opportunities of imaging applications where discriminating colors really matter most

Various forms of organic and inorganic P fertilizers did not negatively affect soil- and root-inhabiting AM fungi in a maize-soybean rotation system.

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Beauregard, M S; Gauthier, M-P; Hamel, C; Zhang, T; Welacky, T; Tan, C S; St-Arnaud, M

2013-02-01

Arbuscular mycorrhizal (AM) fungi are key components of most agricultural ecosystems. Therefore, understanding the impact of agricultural practices on their community structure is essential to improve nutrient mobilization and reduce plant stress in the field. The effects of five different organic or mineral sources of phosphorus (P) for a maize-soybean rotation system on AM fungal diversity in roots and soil were assessed over a 3-year period. Total DNA was extracted from root and soil samples collected at three different plant growth stages. An 18S rRNA gene fragment was amplified and taxa were detected and identified using denaturing gradient gel electrophoresis followed by sequencing. AM fungal biomass was estimated by fatty acid methyl ester analysis. Soil P fertility parameters were also monitored and analyzed for possible changes related with fertilization or growth stages. Seven AM fungal ribotypes were detected. Fertilization significantly modified soil P flux, but had barely any effect on AM fungi community structure or biomass. There was no difference in the AM fungal community between plant growth stages. Specific ribotypes could not be significantly associated to P treatment. Ribotypes were associated with root or soil samples with variable detection frequencies between seasons. AM fungal biomass remained stable throughout the growing seasons. This study demonstrated that roots and soil host distinct AM fungal communities and that these are very temporally stable. The influence of contrasting forms of P fertilizers was not significant over 3 years of crop rotation.

Effect of Seasonal Temperature on the Performance and on the Microbial Community of a Novel AWFR for Decentralized Domestic Wastewater Pretreatment

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Juanhong Li

2017-06-01

Full Text Available Due to environmental burden and human health risks in developing countries, the treatment of decentralized domestic wastewater has been a matter of great concern in recent years. A novel pilot-scale three-stage anaerobic wool-felt filter reactor (AWFR was designed to treat real decentralized domestic wastewater at seasonal temperature variations of 8 to 35 °C for 364 days. The results showed that the average chemical oxygen demand (COD removal efficiencies of AWFR in summer and winter were 76 ± 7.2% and 52 ± 5.9% at one day and three days Hydraulic Retention Time (HRT, respectively. COD mass balance analysis demonstrated that even though COD removal was lower in winter, approximately 43.5% of influent COD was still converted to methane. High-throughput MiSeq sequencing analyses indicated that Methanosaeta, Methanobacterium, and Methanolinea were the predominant methanogens, whereas the genus Bacillus probably played important roles in fermentation processes throughout the whole operation period. The performance and microbial community composition study suggested the application potential of the AWFR system for the pretreatment of decentralized domestic wastewater.

Impact of wheat / faba bean mixed cropping or rotation systems on soil microbial functionalities

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Sanâa Wahbi

2016-09-01

Full Text Available Cropping systems based on carefully designed species mixtures reveal many potential advantages in terms of enhancing crop productivity, reducing pest and diseases and enhacing ecological serices. Associating cereals and legume production either through intercropping or rotations might be a relevant strategy of producing both type of culture, while benefiting from combined nitrogen fixed by the legume through its symbiotic association with nitrogen-fixing bacteria, and from a better use of P and water through mycorrhizal associations. These practices also participate to the diversification of agricultural productions, enabling to secure the regularity of income returns across the seasonal and climatic uncertainties. In this context, we designed a field experiment aiming to estimate the two years impact of these practices on wheat yield and on soil microbial activities as estimated through Substrate Induced Respiration (SIR method and mycorrhizal soil infectivity (MSI measurement. It is expected that understanding soil microbial functionalities in response to these agricultural practices might allows to target the best type of combination, in regard to crop productivity. We found that the tested cropping systems largely impacted soil microbial functionalities and mycorrhizal soil infectivity. Intercropping gave better results in terms of crop productivity than the rotation practice after 2 cropping seasons. Benefits resulting from intercrop should be highly linked with changes recorded on soil microbial functionalities.

Temporal dynamics of bacterial and fungal communities in a genetically modified (GM) rice ecosystem.

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Lee, Seung-Hoon; Kim, Chang-Gi; Kang, Hojeong

2011-04-01

We assessed the temporal dynamics of bacterial and fungal communities in a soil ecosystem supporting genetically modified (GM) rice (Oryza sativa L., ABC-TPSP; fusion of trehalose-6-phosphate synthase and phosphatase). Using terminal restriction fragment length polymorphism analysis and real-time quantitative PCR, we compared bacterial and fungal communities in the soils underlying GM rice (ABC-TPSP), and its host cultivar (Nakdong) during growing seasons and non-growing seasons. Overall, the soils supporting GM and non-GM rice did not differ significantly in diversity indices, including ribotype numbers, for either bacteria or fungi. The diversity index (H) in both the bacterial and fungal communities was correlated with water content, dissolved organic carbon (DOC), and ammonium nitrogen, and the correlation was stronger in fungi than in bacteria. Multivariate analysis showed no differences in microbial community structures between the two crop genotypes, but such differences did appear in time, with significant changes observed after harvest. Gene copy number was estimated as 10(8)~10(11) and 10(5)~10(7) per gram of soil for bacteria and fungi, respectively. As observed for community structure, the rice genotypes did not differ significantly in either bacterial- or fungal-specific gene copy numbers, although we observed a seasonal change in number. We summarize the results of this study as follows. (1) GM rice did not influence soil bacterial and fungal community structures as compared to non-GM rice in our system, (2) both bacterial and fungal communities changed with the growth stage of either rice genotype, (3) fungal communities were less variable than bacterial communities, and (4) although several environmental factors, including ammonium nitrogen and DOC correlated with shifts in microbial community structure, no single factor stood out.

Life in Ice: Microbial Growth Dynamics and Greenhouse Gas Production During Winter in a Thermokarst Bog Revealed by Stable Isotope Probing Targeted Metagenomics

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Blazewicz, S.; White, R. A., III; Tas, N.; Euskirchen, E. S.; Mcfarland, J. W.; Jansson, J.; Waldrop, M. P.

2016-12-01

Permafrost contains a reservoir of frozen C estimated to be twice the size of the current atmospheric C pool. In response to changing climate, permafrost is rapidly warming which could result in widespread seasonal thawing. When permafrost thaws, soils that are rich in ice and C often transform into thermokarst wetlands with anaerobic conditions and significant production of atmospheric CH4. While most C flux research in recently thawed permafrost concentrates on the few summer months when seasonal thaw has occurred, there is mounting evidence that sizeable portions of annual CO2 and CH4 efflux occurs over winter or during a rapid burst of emissions associated with seasonal thaw. A potential mechanism for such efflux patterns is microbial activity in frozen soils over winter where gasses produced are partially trapped within ice until spring thaw. In order to better understand microbial transformation of soil C to greenhouse gas over winter, we applied stable isotope probing (SIP) targeted metagenomics combined with process measurements and field flux data to reveal activities of microbial communities in `frozen' soil from an Alaskan thermokarst bog. Field studies revealed build-up of CO2 and CH4 in frozen soils suggesting that microbial activity persisted throughout the winter in soils poised just below the freezing point. Laboratory incubations designed to simulate in-situ winter conditions (-1.5 °C and anaerobic) revealed continuous CH4 and CO2 production. Strikingly, the quantity of CH4 produced in 6 months in frozen soil was equivalent to approximately 80% of CH4 emitted during the 3 month summer `active' season. Heavy water SIP targeted iTag sequencing revealed growing bacteria and archaea in the frozen anaerobic soil. Growth was primarily observed in two bacterial phyla, Firmicutes and Bacteroidetes, suggesting that fermentation was likely the major C mineralization pathway. SIP targeted metagenomics facilitated characterization of the primary metabolic

Microbial functional diversity associated with plant litter decomposition along a climatic gradient.

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Sherman, Chen; Steinberger, Yosef

2012-08-01

Predicted changes in climate associated with increased greenhouse gas emissions can cause increases in global mean temperature and changes in precipitation regimes. These changes may affect key soil processes, e.g., microbial CO(2) evolution and biomass, mineralization rates, primary productivity, biodiversity, and litter decomposition, which play an important role in carbon and nutrient cycling in terrestrial ecosystems. Our study examined the changes in litter microbial communities and decomposition along a climatic gradient, ranging from arid desert to humid Mediterranean regions in Israel. Wheat straw litter bags were placed in arid, semi-arid, Mediterranean, and humid Mediterranean sites. Samples were collected seasonally over a 2-year period in order to evaluate mass loss, litter moisture, C/N ratio, bacterial colony-forming units (CFUs), microbial CO(2) evolution and biomass, microbial functional diversity, and catabolic profile. Decomposition rate was the highest during the first year of the study at the Mediterranean and arid sites. Community-level physiological profile and microbial biomass were the highest in summer, while bacterial CFUs were the highest in winter. Microbial functional diversity was found to be highest at the humid Mediterranean site, whereas substrate utilization increased at the arid site. Our results support the assumption that climatic factors control litter degradation and regulate microbial activity.

Soil microbial diversity in the vicinity of desert shrubs.

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Saul-Tcherkas, Vered; Unc, Adrian; Steinberger, Yosef

2013-04-01

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0-10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon-Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.

Structure of pelagic microbial assemblages in European mountain lakes during ice-free season

Czech Academy of Sciences Publication Activity Database

Straškrábová, Viera; Bertoni, R.; Blažo, M.; Callieri, C.; Forsström, L.; Fott, J.; Kernan, M.; Macek, Miroslav; Stuchlík, E.; Tolotti, M.

2009-01-01

Roč. 62, - (2009), s. 19-53 ISSN 1612-166X Grant - others:EU MOLAR(CZ) ENV4-CT95-0007; EU EMERGE(CZ) EVK1-CT-1999-00032 Institutional research plan: CEZ:AV0Z60170517; CEZ:AV0Z6017912 Keywords : plankton * mountain lakes * microbial loop Subject RIV: EH - Ecology, Behaviour

Seasonal effects in a lake sediment archaeal community of the Brazilian Savanna.

Science.gov (United States)

Rodrigues, Thiago; Catão, Elisa; Bustamante, Mercedes M C; Quirino, Betania F; Kruger, Ricardo H; Kyaw, Cynthia M

2014-01-01

The Cerrado is a biome that corresponds to 24% of Brazil's territory. Only recently microbial communities of this biome have been investigated. Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes. Analysis revealed marked differences between the archaeal communities found in the two seasons. I.1a and I.1c Thaumarchaeota were found in greater numbers in the transition period, while MCG Archaea was dominant on the dry season. Methanogens were only found in the dry season. Analysis of 16S rRNA sequences revealed lower diversity on the transition period. We detected archaeal amoA sequences in both seasons, but there were more OTUs during the dry season. These sequences were within the same cluster as Nitrosotalea devanaterra's amoA gene. The principal coordinate analysis (PCoA) test revealed significant differences between samples from different seasons. These results provide information on archaeal diversity in freshwater lake sediments of the Cerrado and indicates that rain is likely a factor that impacts these communities.

Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands

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Chelsea J Carey

2015-05-01

Full Text Available Global and regional environmental changes often co-occur, creating complex gradients of disturbance on the landscape. Soil microbial communities are an important component of ecosystem response to environmental change, yet little is known about how microbial structure and function respond to multiple disturbances, or whether multiple environmental changes lead to unanticipated interactive effects. Our study used experimental semi-arid grassland plots in a Mediterranean-climate to determine how soil microbial communities in a seasonally variable ecosystem respond to one, two, or three simultaneous environmental changes: exotic plant invasion, plant invasion + vegetation clipping (to simulate common management practices like mowing or livestock grazing, plant invasion + nitrogen (N fertilization, and plant invasion + clipping + N fertilization. We examined microbial community structure 5-6 years after plot establishment via sequencing of >1 million 16S rRNA genes. Abiotic soil properties (soil moisture, temperature, pH, and inorganic N and microbial functioning (nitrification and denitrification potentials were also measured and showed treatment-induced shifts, including altered NO3- availability, temperature, and nitrification potential. Despite these changes, bacterial and archaeal communities showed little variation in composition and diversity across treatments. Even communities in plots exposed to three interacting environmental changes were similar to those in restored native grassland plots. Historical exposure to large seasonal and inter-annual variations in key soil properties, in addition to prior site cultivation, may select for a functionally plastic or largely dormant microbial community, resulting in a microbial community that is structurally robust to single and multiple environmental changes.

Effects of vegetation type on microbial biomass carbon and nitrogen in subalpine mountain forest soils.

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Ravindran, Anita; Yang, Shang-Shyng

2015-08-01

Microbial biomass plays an important role in nutrient transformation and conservation of forest and grassland ecosystems. The objective of this study was to determine the microbial biomass among three vegetation types in subalpine mountain forest soils of Taiwan. Tatachia is a typical high-altitude subalpine temperate forest ecosystem in Taiwan with an elevation of 1800-3952 m and consists of three vegetation types: spruce, hemlock, and grassland. Three plots were selected in each vegetation type. Soil samples were collected from the organic layer, topsoil, and subsoil. Microbial biomass carbon (Cmic) was determined by the chloroform fumigation-extraction method, and microbial biomass nitrogen (Nmic) was determined from the total nitrogen (Ntot) released during fumigation-extraction. Bacteria, actinomycetes, fungi, cellulolytic microbes, phosphate-solubilizing microbes, and nitrogen-fixing microbes were also counted. The Cmic and Nmic were highest in the surface soil and declined with the soil depth. These were also highest in spruce soils, followed by in hemlock soils, and were lowest in grassland soils. Cmic and Nmic had the highest values in the spring season and the lowest values in the winter season. Cmic and Nmic had significantly positive correlations with total organic carbon (Corg) and Ntot. Contributions of Cmic and Nmic, respectively, to Corg and Ntot indicated that the microbial biomass was immobilized more in spruce and hemlock soils than in grassland soils. Microbial populations of the tested vegetation types decreased with increasing soil depth. Cmic and Nmic were high in the organic layer and decreased with the depth of layers. These values were higher for spruce and hemlock soils than for grassland soils. Positive correlations were observed between Cmic and Nmic and between Corg and Ntot. Copyright © 2014. Published by Elsevier B.V.

The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation.

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Jack A Gilbert

Full Text Available How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure within the bacterial community, with diversity negatively correlated with day-length. Here we determine whether metagenomes and metatranscriptomes follow similar patterns. We generated 16S rRNA datasets, metagenomes (1.2 GB and metatranscriptomes (157 MB for eight additional time points sampled in 2008, representing three seasons (Winter, Spring, Summer and including day and night samples. This is the first microbial 'multi-omic' study to combine 16S rRNA amplicon sequencing with metagenomic and metatranscriptomic profiling. Five main conclusions can be drawn from analysis of these data: 1 Archaea follow the same seasonal patterns as Bacteria, but show lower relative diversity; 2 Higher 16S rRNA diversity also reflects a higher diversity of transcripts; 3 Diversity is highest in winter and at night; 4 Community-level changes in 16S-based diversity and metagenomic profiles are better explained by seasonal patterns (with samples closest in time being most similar, while metatranscriptomic profiles are better explained by diel patterns and shifts in particular categories (i.e., functional groups of genes; 5 Changes in key genes occur among seasons and between day and night (i.e., photosynthesis; but these samples contain large numbers of orphan genes without known homologues and it is these unknown gene sets that appear to contribute most towards defining the differences observed between times. Despite the huge diversity of these microbial communities, there are clear signs of predictable patterns and detectable stability over time. Renewed and intensified efforts are required to reveal fundamental deterministic patterns in the most complex microbial communities. Further, the presence of a substantial proportion of orphan

Coupling of microbial nitrogen transformations and climate in sclerophyll forest soils from the Mediterranean Region of central Chile.

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Pérez, Cecilia A; Armesto, Juan J

2018-06-01

The Mediterranean region of central Chile is experiencing extensive "mega-droughts" with detrimental effects for the environment and economy of the region. In the northern hemisphere, nitrogen (N) limitation of Mediterranean ecosystems has been explained by the decoupling between N inputs and plant uptake during the dormant season. In central Chile, soils have often been considered N-rich in comparison to other Mediterranean ecosystems of the world, yet the impacts of expected intensification of seasonal drought remain unknown. In this work, we seek to disentangle patterns of microbial N transformations and their seasonal coupling with climate in the Chilean sclerophyll forest-type. We aim to assess how water limitation affects microbial N transformations, thus addressing the impact of ongoing regional climate trends on soil N status. We studied four stands of the sclerophyll forest-type in Chile. Field measurements in surface soils showed a 67% decline of free-living diazotrophic activity (DA) and 59% decrease of net N mineralization rates during the summer rainless and dormant season, accompanied by a stimulation of in-situ denitrification rates to values 70% higher than in wetter winter. Higher rates of both free-living DA and net N mineralization found during spring, provided evidence for strong coupling of these two processes during the growing season. Overall, the experimental addition of water in the field to litter samples almost doubled DA but had no effect on denitrification rates. We conclude that coupling of microbial mediated soil N transformations during the wetter growing season explains the N enrichment of sclerophyll forest soils. Expected increases in the length and intensity of the dry period, according to climate change models, reflected in the current mega-droughts may drastically reduce biological N fixation and net N mineralization, increasing at the same time denitrification rates, thereby potentially reducing long-term soil N capital

Seasonal Effects in a Lake Sediment Archaeal Community of the Brazilian Savanna

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Thiago Rodrigues

2014-01-01

Full Text Available The Cerrado is a biome that corresponds to 24% of Brazil’s territory. Only recently microbial communities of this biome have been investigated. Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes. Analysis revealed marked differences between the archaeal communities found in the two seasons. I.1a and I.1c Thaumarchaeota were found in greater numbers in the transition period, while MCG Archaea was dominant on the dry season. Methanogens were only found in the dry season. Analysis of 16S rRNA sequences revealed lower diversity on the transition period. We detected archaeal amoA sequences in both seasons, but there were more OTUs during the dry season. These sequences were within the same cluster as Nitrosotalea devanaterra’s amoA gene. The principal coordinate analysis (PCoA test revealed significant differences between samples from different seasons. These results provide information on archaeal diversity in freshwater lake sediments of the Cerrado and indicates that rain is likely a factor that impacts these communities.

Are variations in heterotrophic soil respiration related to changes in substrate availability and microbial biomass carbon in the subtropical forests?

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Wei, Hui; Chen, Xiaomei; Xiao, Guoliang; Guenet, Bertrand; Vicca, Sara; Shen, Weijun

2015-01-01

Soil temperature and moisture are widely-recognized controlling factors on heterotrophic soil respiration (Rh), although they often explain only a portion of Rh variability. How other soil physicochemical and microbial properties may contribute to Rh variability has been less studied. We conducted field measurements on Rh half-monthly and associated soil properties monthly for two years in four subtropical forests of southern China to assess influences of carbon availability and microbial properties on Rh. Rh in coniferous forest was significantly lower than that in the other three broadleaf species-dominated forests and exhibited obvious seasonal variations in the four forests (P < 0.05). Temperature was the primary factor influencing the seasonal variability of Rh while moisture was not in these humid subtropical forests. The quantity and decomposability of dissolved organic carbon (DOC) were significantly important to Rh variations, but the effect of DOC content on Rh was confounded with temperature, as revealed by partial mantel test. Microbial biomass carbon (MBC) was significantly related to Rh variations across forests during the warm season (P = 0.043). Our results suggest that DOC and MBC may be important when predicting Rh under some conditions, and highlight the complexity by mutual effects of them with environmental factors on Rh variations. PMID:26670822

Microbial and geochemical assessment of bauxitic un-mined and post-mined chronosequence soils from Mocho Mountains, Jamaica.

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Lewis, Dawn E; Chauhan, Ashvini; White, John R; Overholt, Will; Green, Stefan J; Jasrotia, Puja; Wafula, Denis; Jagoe, Charles

2012-10-01

Microorganisms are very sensitive to environmental change and can be used to gauge anthropogenic impacts and even predict restoration success of degraded environments. Here, we report assessment of bauxite mining activities on soil biogeochemistry and microbial community structure using un-mined and three post-mined sites in Jamaica. The post-mined soils represent a chronosequence, undergoing restoration since 1987, 1997, and 2007. Soils were collected during dry and wet seasons and analyzed for pH, organic matter (OM), total carbon (TC), nitrogen (TN), and phosphorus. The microbial community structure was assessed through quantitative PCR and massively parallel bacterial ribosomal RNA (rRNA) gene sequencing. Edaphic factors and microbial community composition were analyzed using multivariate statistical approaches and revealed a significant, negative impact of mining on soil that persisted even after greater than 20 years of restoration. Seasonal fluctuations contributed to variation in measured soil properties and community composition, but they were minor in comparison to long-term effects of mining. In both seasons, post-mined soils were higher in pH but OM, TC, and TN decreased. Bacterial rRNA gene analyses demonstrated a general decrease in diversity in post-mined soils and up to a 3-log decrease in rRNA gene abundance. Community composition analyses demonstrated that bacteria from the Proteobacteria (α, β, γ, δ), Acidobacteria, and Firmicutes were abundant in all soils. The abundance of Firmicutes was elevated in newer post-mined soils relative to the un-mined soil, and this contrasted a decrease, relative to un-mined soils, in proteobacterial and acidobacterial rRNA gene abundances. Our study indicates long-lasting impacts of mining activities to soil biogeochemical and microbial properties with impending loss in soil productivity.

Sub-soil microbial activity under rotational cotton crops in Australia

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Polain, Katherine; Knox, Oliver; Wilson, Brian; Pereg, Lily

2016-04-01

Soil microbial communities contribute significantly to soil organic matter formation, stabilisation and destabilisation, through nutrient cycling and biodegradation. The majority of soil microbial research examines the processes occurring in the top 0 cm to 30 cm of the soil, where organic nutrients are easily accessible. In soils such as Vertosols, the high clay content causes swelling and cracking. When soil cracking is coupled with rain or an irrigation event, a flush of organic nutrients can move down the soil profile, becoming available for subsoil microbial community use and potentially making a significant contribution to nutrient cycling and biodegradation in soils. At present, the mechanisms and rates of soil nutrient turnover (such as carbon and nitrogen) at depth under cotton rotations are mostly speculative and the process-response relationships remain unclear, although they are undoubtedly underpinned by microbial activity. Our research aims to determine the contribution and role of soil microbiota to the accumulation, cycling and mineralisation of carbon and nitrogen through the whole root profile under continuous cotton (Gossypium hirsutum) and cotton-maize rotations in regional New South Wales, Australia. Through seasonal work, we have established both baseline and potential microbial activity rates from 0 cm to 100 cm down the Vertosol profile, using respiration and colourimetric methods. Further whole soil profile analyses will include determination of microbial biomass and isotopic carbon signatures using phospholipid fatty acid (PLFA) methodology, identification of microbial communities (sequencing) and novel experiments to investigate potential rates of nitrogen mineralisation and quantification of associated genes. Our preliminary observations and the hypotheses tested in this three-year study will be presented.

Living Dendrolitic Microbial Mats in Hamelin Pool, Shark Bay, Western Australia

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Erica P. Suosaari

2018-06-01

Full Text Available Hamelin Pool, Shark Bay, Western Australia, is home to the largest and most diverse assemblage of living marine stromatolites, with shapes and sizes comparable to ancient structures. A recent field-intensive program revealed seasonally ephemeral occurrences of modern dendrolitic microbial mats forming in intertidal, low energy settings. Dominated by filamentous cyanobacteria, dendrolitic microbial mats are formed when filaments provide a supporting framework as a result of gliding mobility, to build a shrubby morphology. Dendrolites, known throughout the rock record, refer to macroscopic microbialites with mesostuctures composed of unlaminated arborescent structures called shrubs. In these modern examples, thick filaments of Lyngbya aestuarii form the “trunk” of the bush, with finer filaments of Lyngbya fragilis, Phormidium sp. and Schizothrix sp. forming the “branches” These biologically-influenced dendrolitic structures provide insight into the complex interplay of microbial communities and the environment, broadening our understanding of shrub and dendrolite formation throughout the rock record.

Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability.

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James R White

Full Text Available BACKGROUND: Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge "holobiont" system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown. METHODOLOGY/PRINCIPAL FINDINGS: We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata, from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs. Approximately 65,550 rRNA sequences (24% could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species (Amphimedon compressa, and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata-specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata, comprising >34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described. CONCLUSIONS/SIGNIFICANCE: Slight shifts in several bacterial taxa

The hidden seasonality of the rare biosphere in coastal marine bacterioplankton

KAUST Repository

Alonso-Sáez, Laura

2015-04-08

Summary: Rare microbial taxa are increasingly recognized to play key ecological roles, but knowledge of their spatio-temporal dynamics is lacking. In a time-series study in coastal waters, we detected 83 bacterial lineages with significant seasonality, including environmentally relevant taxa where little ecological information was available. For example, Verrucomicrobia had recurrent maxima in summer, while the Flavobacteria NS4, NS5 and NS2b clades had contrasting seasonal niches. Among the seasonal taxa, only 4 were abundant and persistent, 20 cycled between rare and abundant and, remarkably, most of them (59) were always rare (contributing <1% of total reads). We thus demonstrate that seasonal patterns in marine bacterioplankton are largely driven by lineages that never sustain abundant populations. A fewer number of rare taxa (20) also produced episodic \\'blooms\\', and these events were highly synchronized, mostly occurring on a single month. The recurrent seasonal growth and loss of rare bacteria opens new perspectives on the temporal dynamics of the rare biosphere, hitherto mainly characterized by dormancy and episodes of \\'boom and bust\\', as envisioned by the seed-bank hypothesis. The predictable patterns of seasonal reoccurrence are relevant for understanding the ecology of rare bacteria, which may include key players for the functioning of marine ecosystems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Effects of reforestation on ammonia-oxidizing microbial community composition and abundance in subtropical acidic forest soils.

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Wu, Ruo-Nan; Meng, Han; Wang, Yong-Feng; Gu, Ji-Dong

2018-06-01

Forest ecosystems have great ecological values in mitigation of climate change and protection of biodiversity of flora and fauna; re-forestry is commonly used to enhance the sequestration of atmospheric CO 2 into forest storage biomass. Therefore, seasonal and spatial dynamics of the major microbial players in nitrification, ammonia-oxidizing archaea (AOA) and bacteria (AOB), in acidic soils of young and matured revegetated forests were investigated to elucidate the changes of microbial communities during forest restoration, and compared to delineate the patterns of community shifts under the influences of environmental factors. AOA were more abundant than AOB in both young and matured revegetated forest soils in both summer and winter seasons. In summer, however, the abundance of amoA-AOA decreased remarkably (p < 0.01), ranging from 1.90 (± 0.07) × 10 8 copies per gram dry soil in matured forest to 5.04 (± 0.43) × 10 8 copies per gram dry soil in young forest, and amoA-AOB was below detection limits to obtain any meaningful values. Moreover, exchangeable Al 3+ and organic matter were found to regulate the physiologically functional nitrifiers, especially AOA abundance in acidic forest soils. AOB community in winter showed stronger correlation with the restoration status of revegetated forests and AOA community dominated by Nitrosotalea devanaterra, in contrast, was more sensitive to the seasonal and spatial variations of environmental factors. These results enrich the current knowledge of nitrification during re-forestry and provide valuable information to developmental status of revegetated forests for management through microbial analysis.

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali.

Directory of Open Access Journals (Sweden)

Benjamin J Krajacich

Full Text Available The poorly understood mechanisms of dry season persistence of Anopheles spp. mosquitoes through the dry season in Africa remain a critical gap in our knowledge of Plasmodium disease transmission. While it is thought that adult mosquitoes remain in a dormant state throughout this seven-month dry season, the nature of this state remains unknown and has largely not been recapitulated in laboratory settings. To elucidate possible connections of this state with microbial composition, the whole body microbiomes of adult mosquitoes in the dry and wet seasons in two locations of Mali with varying water availability were compared by sequencing the 16S ribosomal RNA gene. These locations were a village near the Niger River with year-round water sources (N'Gabakoro, "riparian", and a typical Sahelian area with highly seasonal breeding sites (Thierola Area, "Sahelian". The 16S bacterial data consisted of 2057 sequence variants in 426 genera across 184 families. From these data, we found several compositional differences that were seasonally and spatially linked. Counter to our initial hypothesis, there were more pronounced seasonal differences in the bacterial microbiome of riparian, rather than Sahelian areas. These seasonal shifts were primarily in Ralstonia, Sphingorhabdus, and Duganella spp. bacteria that are usually soil and water-associated, indicating these changes may be from bacteria acquired in the larval environment, rather than adulthood. In Sahelian dry season mosquitoes, there was a unique intracellular bacteria, Anaplasma, which likely was acquired through non-human blood feeding. Cytochrome B analysis of blood meals showed greater heterogeneity in host choice of An. coluzzii independent of season in the Thierola area compared to N'Gabakoro (77.5% vs. 94.6% human-origin blood meal, respectively, indicating a relaxation of anthropophily. Overall, this exploratory study provides valuable indications of spatial and seasonal differences in

Life under ice: Investigating microbial-related biogeochemical cycles in the seasonally-covered Great Lake Onego, Russia

Science.gov (United States)

Thomas, Camille; Ariztegui, Daniel; Victor, Frossard; Emilie, Lyautey; Marie-Elodie, Perga; Life Under Ice Scientific Team

2016-04-01

The Great European lakes Ladoga and Onego are important resources for Russia in terms of drinking water, energy, fishing and leisure. Because their northern location (North of Saint Petersburgh), these lakes are usually ice-covered during winter. Due to logistical reasons, their study has thus been limited to the ice-free periods, and very few data are available for the winter season. As a matter of fact, comprehension of large lakes behaviour in winter is very limited as compared to the knowledge available from small subpolar lakes or perennially ice-covered polar lakes. To tackle this issue, an international consortium of scientists has gathered around the « life under ice » project to investigate physical, chemical and biogeochemical changes during winter in Lake Onego. Our team has mainly focused on the characterization and quantification of biological processes, from the water column to the sediment, with a special focus on methane cycling and trophic interactions. A first « on-ice » campaign in March 2015 allowed the sampling of a 120 cm sedimentary core and the collection of water samples at multiple depths. The data resulting from this expedition will be correlated to physical and chemical parameters collected simultaneously. A rapid biological activity test was applied immediately after coring in order to test for microbial activity in the sediments. In situ adenosine-5'-triphosphate (ATP) measurements were carried out in the core and taken as an indication of living organisms within the sediments. The presence of ATP is a marker molecule for metabolically active cells, since it is not known to form abiotically. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) were extracted from these samples, and quantified. Quantitative polymerase chain reactions (PCR) were performed on archaeal and bacterial 16S rRNA genes used to reconstruct phylogenies, as well as on their transcripts. Moreover, functional genes involved in the methane and nitrogen cycles

Microbial-meiofaunal interrelationships in coastal sediments of the Red Sea.

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El-Serehy, Hamed A; Al-Rasheid, Khaled A; Al-Misned, Fahad A; Al-Talasat, Abdul Allah R; Gewik, Mohamed M

2016-05-01

Population density and biomass of bacteria and meiofauna were investigated seasonally in the sediments of the north-western bank of Red Sea. Samples of sediments were collected seasonally from three different stations to determine microphytobenthic biomass (chlorophyll a), protein, lipid, carbohydrate, and total organic matter concentrations. These investigations revealed that microbial components tended to increase their dominancy, whereas sensitive meiofauna were extremely reduced during the entire study period. Thus a very low density of the total meiofauna (with an annual average of 109 ± 26 ind./10 cm(2)) was recorded whilst the benthic microbial population densities exhibited higher values (ranging from 0.31 ± 0.02 × 10(8) to 43.67 ± 18.62 × 10(8)/g dry sediment). These changes in the relative importance analysis of benthic microbial components versus meiofaunal ones seem to be based on the impact of organic matter accumulation on the function and structure of these benthic communities. Proteins, lipids and carbohydrates showed very low concentration values, and the organic matter mostly consisted of carbohydrates, reflecting lower nutritional values for benthic fauna in general and meiofauna in particular. The distribution of microbial and meiofaunal communities seems to be dependent on the quality of the organic matter rather than on its quantity. Total organic matter concentrations varied between 5.8 and 7.6 mg/g, with organic carbon accounting for only 32% of the total organic matter. Chlorophyll a attained very low values, fluctuating between 0.11 and 0.56 μg/g, indicating the oligotrophy of the studied area. The very low concentration of chlorophyll a in the Red Sea sediment suggests that the sedimentary organic matter, heterotrophic bacteria and/or protozoa constitute an alternative resource that is consumed by meiofauna when algae are less abundant. Protozoa, therefore, represent the "missing link in bacteria-meiofauna interaction

The microbial fate of carbon in high-latitude seas: Impact of the microbial loop on oceanic uptake of CO{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Yager, P.L.

1996-12-31

This dissertation examines pelagic microbial processes in high-latitude seas, how they affect regional and global carbon cycling, and how they might respond to hypothesized changes in climate. Critical to these interests is the effect of cold temperature on bacterial activity. Also important is the extent to which marine biological processes in general impact the inorganic carbon cycle. The study area is the Northeast Water (NEW) Polynya, a seasonally-recurrent opening in the permanent ice situated over the northeastern Greenland continental shelf. This work was part of an international, multi-disciplinary research project studying carbon cycling in the coastal Arctic. The first chapter describes a simple model which links a complex marine food web to a simplified ocean and atmosphere. The second chapter investigates the inorganic carbon inventory of the summertime NEW Polynya surface waters to establish the effect of biological processes on the air-sea pCO{sub 2} gradient. The third and fourth chapters use a kinetic approach to examine microbial activities in the NEW Polynya as a function of temperature and dissolved organic substrate concentration, testing the so-called Pomeroy hypothesis that microbial activity is disproportionately reduced at low environmental temperatures owing to increased organic substrate requirements. Together, the suite of data collected on microbial activities, cell size, and grazing pressure suggest how unique survival strategies adopted by an active population of high-latitude bacteria may contribute to, rather than detract from, an efficient biological carbon pump.

Microbial deterioration of Mayan stone buildings at Uxmal, Yucatan, Mexico

International Nuclear Information System (INIS)

Ortega-Morales, O.; Guezennec, J.; Hernandez D, G.; Jozsa, P.; Sand, W.; Crassous, P.

1998-01-01

The microbial communities associated to Uxmal Mayan monuments (Yucatan, Mexico) and their role in stone deterioration were preliminary characterized by chemical, biochemical, microbiological, microscopical and surface analysis methods under two climatic seasons (1997). The organic matter and organic carbon and nitrogen were in the range of those reported for other stone buildings, indicating that oligo trophic conditions prevail at Uxmal. Quantitative differences in microbial biomass was higher at indoor section were the organic matter content was the highest and micro-environmental conditions (availability of water and protection to direct sunlight) are more suitable for microbial growth. The microbiological analysis underestimated the microbial biomass, as revealed by biochemical approaches. Nitrate and nitrite-oxidizing, metilotrophic and heterotrophic bacteria and fungi were detected in most surfaces. The heterotrophic bacteria were the most abundant microbial group (microbiological data). However, the chlorophyll profiles and Scanning Electron Microscopy showed that the microalgae are the most abundant colonizers in Uxmal stone buildings. EDAX analysis showed that the most surfaces were covered by an organic layer (cells and exo polymers). Gypsum was found in few samples. The large photo trophic biomass seems to play a role in stone bio deterioration by supporting growth of heterotrophic microorganisms (bacteria and fungi) which are known to produce organic acids leading to calcite dissolution and cations chelation. Further studies are being carried out in order to determine the role of exo polysaccharides which are thought to play a role in chemical degradation of limestone substrates in Uxmal. (Author)

Winter ecology of a subalpine grassland: Effects of snow removal on soil respiration, microbial structure and function.

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Gavazov, Konstantin; Ingrisch, Johannes; Hasibeder, Roland; Mills, Robert T E; Buttler, Alexandre; Gleixner, Gerd; Pumpanen, Jukka; Bahn, Michael

2017-07-15

Seasonal snow cover provides essential insulation for mountain ecosystems, but expected changes in precipitation patterns and snow cover duration due to global warming can influence the activity of soil microbial communities. In turn, these changes have the potential to create new dynamics of soil organic matter cycling. To assess the effects of experimental snow removal and advanced spring conditions on soil carbon (C) and nitrogen (N) dynamics, and on the biomass and structure of soil microbial communities, we performed an in situ study in a subalpine grassland in the Austrian Alps, in conjunction with soil incubations under controlled conditions. We found substantial winter C-mineralisation and high accumulation of inorganic and organic N in the topsoil, peaking at snowmelt. Soil microbial biomass doubled under the snow, paralleled by a fivefold increase in its C:N ratio, but no apparent change in its bacteria-dominated community structure. Snow removal led to a series of mild freeze-thaw cycles, which had minor effects on in situ soil CO 2 production and N mineralisation. Incubated soil under advanced spring conditions, however, revealed an impaired microbial metabolism shortly after snow removal, characterised by a limited capacity for C-mineralisation of both fresh plant-derived substrates and existing soil organic matter (SOM), leading to reduced priming effects. This effect was transient and the observed recovery in microbial respiration and SOM priming towards the end of the winter season indicated microbial resilience to short-lived freeze-thaw disturbance under field conditions. Bacteria showed a higher potential for uptake of plant-derived C substrates during this recovery phase. The observed temporary loss in microbial C-mineralisation capacity and the promotion of bacteria over fungi can likely impede winter SOM cycling in mountain grasslands under recurrent winter climate change events, with plausible implications for soil nutrient availability and

Rate of litter decomposition and microbial activity in an area of Caatinga

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Patrícia Carneiro Souto

2013-12-01

Full Text Available In order to evaluate the decomposition of litter and microbial activity in an area of preserved Caatinga, an experiment was conducted in the Natural Heritage Private Reserve Tamanduá Farm in Santa Terezinha county, State of Paraiba. The decomposition rate was determined by using litter bags containing 30 g of litter, which were arranged on the soil surface in September 2003 and 20 bags were taken each month until September 2005. The collected material was oven dried and weighed to assess weight loss compared to initial weight. Microbial activity was estimated monthly by the quantification of carbon dioxide (CO2 released into the edaphic breathing process from the soil surface, and captured by KOH solution. Weight loss of litter after one year was 41.19% and, after two years, was 48.37%, indicating a faster decomposition in the first year. Data analysis showed the influence of season on litter decomposition and temperature on microbial activity.

Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil

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Jie Chen

2017-07-01

Full Text Available Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD and extending the dry-season duration (ED but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08 was much lower than that of the net N transformation rate (0.55 ± 0.02 throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA and denitrifying genes (nirK, nirS, and nosZ, while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4+ and dissolved organic carbon concentrations] during the experiment.

Feeding behavior, microbial efficiency, and nitrogen balance of Nellore heifers supplemented with crude glycerin

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Gonçalo Mesquita da Silva

2016-09-01

Full Text Available This study aimed to evaluate the inclusion of crude glycerin in diets for Nellore heifers grazing on a Brachiaria brizantha pasture, during the dry season, on urine and plasma urea concentrations, feeding behavior, and microbial protein synthesis. Sixty Nellore heifers with an average initial weight of 285.89 ± 18.74 kg, at approximately 19 ± 2 months of age, were distributed, in a completely randomized design, into the following five treatments with twelve replicates: 0.00, 4.00, 8.00, 12.00, and 16.00% inclusion of crude glycerin in the diet they were fed. Grazing time decreased linearly (P 0.05, averaging 113.73g CP per kg TDN ingested. Plasma nitrogen concentration did not show any effects (P > 0.05, averaging 13.11 mg dL?1. Supplementing heifers during the dry season, at 0.7% BW, using up to 16% crude glycerin in the diet composition, did not elicit positive responses from feeding behavior and had little influence on microbial synthesis.

Shifts of growing-season precipitation peaks decrease soil respiration in a semiarid grassland.

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Ru, Jingyi; Zhou, Yaqiong; Hui, Dafeng; Zheng, Mengmei; Wan, Shiqiang

2018-03-01

Changing precipitation regimes could have profound influences on carbon (C) cycle in the biosphere. However, how soil C release from terrestrial ecosystems responds to changing seasonal distribution of precipitation remains unclear. A field experiment was conducted for 4 years (2013-2016) to examine the effects of altered precipitation distributions in the growing season on soil respiration in a temperate steppe in the Mongolian Plateau. Over the 4 years, both advanced and delayed precipitation peaks suppressed soil respiration, and the reductions mainly occurred in August. The decreased soil respiration could be primarily attributable to water stress and subsequently limited plant growth (community cover and belowground net primary productivity) and soil microbial activities in the middle growing season, suggesting that precipitation amount in the middle growing season is more important than that in the early, late, or whole growing seasons in regulating soil C release in grasslands. The observations of the additive effects of advanced and delayed precipitation peaks indicate semiarid grasslands will release less C through soil respiratory processes under the projected seasonal redistribution of precipitation in the future. Our findings highlight the potential role of intra-annual redistribution of precipitation in regulating ecosystem C cycling in arid and semiarid regions. © 2017 John Wiley & Sons Ltd.

Inferred effects of cloud deposition on forest floor nutrient cycling and microbial properties along a short elevation gradient

International Nuclear Information System (INIS)

Lavoie, M.; Bradley, R.L.

2003-01-01

Higher cloud cover significantly decreases forest floor pH, decrease exchangeable cations, modifies mineral-N speciation and increases physiological stress within microbial communities. - Cloud water deposition often increases with elevation, and it is widely accepted that this cloud water increases acid loading to upland forest ecosystems. A study was undertaken in south-eastern Quebec to determine if a 250 m elevation gradient (i.e. 420-665 m), along a uniform sugar-maple stand on the slope of Mount Orford, corresponded to a pH gradient in the forest floor and to predictable changes in soil nutrient availability and microbial properties. Precipitation data from a nearby study, and a photographic survey, provided presumptive evidence that this elevation gradient corresponded to a strong gradient in cloud water deposition. Forest floor temperature did not differ significantly across elevations. Forest floor moisture content was significantly higher, whereas pH and exchangeable Ca and Mg were significantly lower, at the higher elevations. Average seasonal net nitrification rates, determined by long-term laboratory incubations, did not differ significantly across elevations, whereas average seasonal net ammonification rates were significantly higher at higher elevations. Basal respiration rates and microbial biomass did not differ significantly across elevations, but metabolic quotient was significantly higher at higher elevations indicating possible environmental stress on forest floor microbial communities due to cloud water deposition. Anaerobic N mineralisation rates were significantly higher at higher elevations suggesting that N-limited microbial communities frequently exposed to cloud cover can be important short-term sinks for atmospheric N, thereby contributing to increase the active-N fraction of forest floors. We conclude that, where no significant changes in vegetation or temperature occur, elevation gradients can still be used to understand the spatial

Water type and irrigation time effects on microbial metabolism of a soil cultivated with Bermuda-grass Tifton 85

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Sandra Furlan Nogueira

2011-06-01

Full Text Available This study investigated the microbial metabolism in Bermuda-grass Tifton 85 areas after potable-water and effluent irrigation treatments. The experiment was carried out in Lins/SP with samples taken in the rainy and dry seasons (2006 after one year and three years of irrigation management, and set up on an entirely randomized block design with four treatments: C (control, without irrigation or fertilization, PW (potable water + 520 kg of N ha-1 year-1; TE3 and TE0 (treated effluent + 520 kg of N ha-1 year-1 for three years and one year, respectively. The parameters determined were: microbial biomass carbon, microbial activity, and metabolic quotient. Irrigation with wastewater after three years indicated no alteration in soil quality for C and ET3; for PW, a negative impact on soil quality (microbial biomass decrease suggested that water-potable irrigation in Lins is not an adequate option. Microbial activity alterations observed in TE0 characterize a priming effect.

Soil ecology of a rock outcrop ecosystem: Abiotic stresses, soil respiration, and microbial community profiles in limestone cedar glades

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Cartwright, Jennifer M.; Advised by Dzantor, E. Kudjo

2015-01-01

Limestone cedar glades are a type of rock outcrop ecosystem characterized by shallow soil and extreme hydrologic conditions—seasonally ranging from xeric to saturated—that support a number of plant species of conservation concern. Although a rich botanical literature exists on cedar glades, soil biochemical processes and the ecology of soil microbial communities in limestone cedar glades have largely been ignored. This investigation documents the abiotic stress regime of this ecosystem (shallow soil, extreme hydrologic fluctuations and seasonally high soil surface temperatures) as well as soil physical and chemical characteristics, and relates both types of information to ecological structures and functions including vegetation, soil respiration, and soil microbial community metabolic profiles and diversity. Methods used in this investigation include field observations and measurements of soil physical and chemical properties and processes, laboratory analyses, and microbiological assays of soil samples.

Microbial quality of agricultural water in Central Florida

Science.gov (United States)

Topalcengiz, Zeynal; Strawn, Laura K.

2017-01-01

The microbial quality of water that comes into the edible portion of produce is believed to directly relate to the safety of produce, and metrics describing indicator organisms are commonly used to ensure safety. The US FDA Produce Safety Rule (PSR) sets very specific microbiological water quality metrics for agricultural water that contacts the harvestable portion of produce. Validation of these metrics for agricultural water is essential for produce safety. Water samples (500 mL) from six agricultural ponds were collected during the 2012/2013 and 2013/2014 growing seasons (46 and 44 samples respectively, 540 from all ponds). Microbial indicator populations (total coliforms, generic Escherichia coli, and enterococci) were enumerated, environmental variables (temperature, pH, conductivity, redox potential, and turbidity) measured, and pathogen presence evaluated by PCR. Salmonella isolates were serotyped and analyzed by pulsed-field gel electrophoresis. Following rain events, coliforms increased up to 4.2 log MPN/100 mL. Populations of coliforms and enterococci ranged from 2 to 8 and 1 to 5 log MPN/100 mL, respectively. Microbial indicators did not correlate with environmental variables, except pH (P<0.0001). The invA gene (Salmonella) was detected in 26/540 (4.8%) samples, in all ponds and growing seasons, and 14 serotypes detected. Six STEC genes were detected in samples: hly (83.3%), fliC (51.8%), eaeA (17.4%), rfbE (17.4%), stx-I (32.6%), stx-II (9.4%). While all ponds met the PSR requirements, at least one virulence gene from Salmonella (invA-4.8%) or STEC (stx-I-32.6%, stx-II-9.4%) was detected in each pond. Water quality for tested agricultural ponds, below recommended standards, did not guarantee the absence of pathogens. Investigating the relationships among physicochemical attributes, environmental factors, indicator microorganisms, and pathogen presence allows researchers to have a greater understanding of contamination risks from agricultural surface

Microbial quality of agricultural water in Central Florida.

Directory of Open Access Journals (Sweden)

Zeynal Topalcengiz

Full Text Available The microbial quality of water that comes into the edible portion of produce is believed to directly relate to the safety of produce, and metrics describing indicator organisms are commonly used to ensure safety. The US FDA Produce Safety Rule (PSR sets very specific microbiological water quality metrics for agricultural water that contacts the harvestable portion of produce. Validation of these metrics for agricultural water is essential for produce safety. Water samples (500 mL from six agricultural ponds were collected during the 2012/2013 and 2013/2014 growing seasons (46 and 44 samples respectively, 540 from all ponds. Microbial indicator populations (total coliforms, generic Escherichia coli, and enterococci were enumerated, environmental variables (temperature, pH, conductivity, redox potential, and turbidity measured, and pathogen presence evaluated by PCR. Salmonella isolates were serotyped and analyzed by pulsed-field gel electrophoresis. Following rain events, coliforms increased up to 4.2 log MPN/100 mL. Populations of coliforms and enterococci ranged from 2 to 8 and 1 to 5 log MPN/100 mL, respectively. Microbial indicators did not correlate with environmental variables, except pH (P<0.0001. The invA gene (Salmonella was detected in 26/540 (4.8% samples, in all ponds and growing seasons, and 14 serotypes detected. Six STEC genes were detected in samples: hly (83.3%, fliC (51.8%, eaeA (17.4%, rfbE (17.4%, stx-I (32.6%, stx-II (9.4%. While all ponds met the PSR requirements, at least one virulence gene from Salmonella (invA-4.8% or STEC (stx-I-32.6%, stx-II-9.4% was detected in each pond. Water quality for tested agricultural ponds, below recommended standards, did not guarantee the absence of pathogens. Investigating the relationships among physicochemical attributes, environmental factors, indicator microorganisms, and pathogen presence allows researchers to have a greater understanding of contamination risks from agricultural

Microbial quality of agricultural water in Central Florida.

Science.gov (United States)

Topalcengiz, Zeynal; Strawn, Laura K; Danyluk, Michelle D

2017-01-01

The microbial quality of water that comes into the edible portion of produce is believed to directly relate to the safety of produce, and metrics describing indicator organisms are commonly used to ensure safety. The US FDA Produce Safety Rule (PSR) sets very specific microbiological water quality metrics for agricultural water that contacts the harvestable portion of produce. Validation of these metrics for agricultural water is essential for produce safety. Water samples (500 mL) from six agricultural ponds were collected during the 2012/2013 and 2013/2014 growing seasons (46 and 44 samples respectively, 540 from all ponds). Microbial indicator populations (total coliforms, generic Escherichia coli, and enterococci) were enumerated, environmental variables (temperature, pH, conductivity, redox potential, and turbidity) measured, and pathogen presence evaluated by PCR. Salmonella isolates were serotyped and analyzed by pulsed-field gel electrophoresis. Following rain events, coliforms increased up to 4.2 log MPN/100 mL. Populations of coliforms and enterococci ranged from 2 to 8 and 1 to 5 log MPN/100 mL, respectively. Microbial indicators did not correlate with environmental variables, except pH (P<0.0001). The invA gene (Salmonella) was detected in 26/540 (4.8%) samples, in all ponds and growing seasons, and 14 serotypes detected. Six STEC genes were detected in samples: hly (83.3%), fliC (51.8%), eaeA (17.4%), rfbE (17.4%), stx-I (32.6%), stx-II (9.4%). While all ponds met the PSR requirements, at least one virulence gene from Salmonella (invA-4.8%) or STEC (stx-I-32.6%, stx-II-9.4%) was detected in each pond. Water quality for tested agricultural ponds, below recommended standards, did not guarantee the absence of pathogens. Investigating the relationships among physicochemical attributes, environmental factors, indicator microorganisms, and pathogen presence allows researchers to have a greater understanding of contamination risks from agricultural surface

Temporal variability and phylogenetic characterization of planktonic anammox bacteria in the coastal upwelling ecosystem off central Chile

Science.gov (United States)

Galán, Alexander; Molina, Verónica; Belmar, Lucy; Ulloa, Osvaldo

2012-01-01

The phylogenetic affiliation and temporal variability in the abundance of planktonic anammox bacteria were studied at a time-series station above the continental shelf off central Chile (∼36°S; bottom depth 93 m), a wind-driven, seasonal upwelling area, between August 2006 and April 2008. The study was carried out by cloning and sequencing the 16S rRNA gene and by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Our results showed the presence of a single anammox bacteria-like ribotype during both upwelling and non-upwelling seasons, which was phylogenetically associated with a recently described oxygen-minimum-zone subcluster within the Candidatus Scalindua clade. Moreover, clear differences were observed in the temporal and vertical distribution of anammox cells. During the upwelling season (austral spring-summer), relatively high abundances (∼5500 cells mL -1) and large cells (0.8 μm 3-75.7 fg C cell -1) were found below 20 m depth. In contrast, during the non-upwelling season (austral fall-winter), lower abundances (∼600 cells mL -1) and smaller cells (0.1 μm 3-22.8 fg C cell -1) were found, predominantly associated with the bottom layer. Overall, our results indicate that the abundance and vertical distribution of anammox planktonic assemblages are related to the occurrence of seasonal, wind-driven, coastal upwelling, which in turn appears to offer favorable conditions for the development of these microorganisms. The dominance of a unique anammox bacteria-like ribotype could be related to the high environmental variability observed in the system, which prevents the establishment of other anammox lineages.

Abundance and biomass responses of microbial food web components to hydrology and environmental gradients within a floodplain of the River Danube.

Science.gov (United States)

Palijan, Goran

2012-07-01

This study investigated the relationships of time-dependent hydrological variability and selected microbial food web components. Samples were collected monthly from the Kopački Rit floodplain in Croatia, over a period of 19 months, for analysis of bacterioplankton abundance, cell size and biomass; abundance of heterotrophic nanoflagellates and nanophytoplankton; and concentration of chlorophyll a. Similar hydrological variability at different times of the year enabled partition of seasonal effects from hydrological changes on microbial community properties. The results suggested that, unlike some other studies investigating sites with different connectivity, bacterioplankton abundance, and phytoplankton abundance and biomass increased during lentic conditions. At increasing water level, nanophytoplankton showed lower sensitivity to disturbance in comparison with total phytoplankton biomass: this could prolong autotrophic conditions within the floodplain. Bacterioplankton biomass, unlike phytoplankton, was not impacted by hydrology. The bacterial biomass less affected by hydrological changes can be an important additional food component for the floodplain food web. The results also suggested a mechanism controlling bacterial cell size independent of hydrology, as bacterial cell size was significantly decreased as nanoflagellate abundance increased. Hydrology, regardless of seasonal sucession, has the potential to structure microbial food webs, supporting microbial development during lentic conditions. Conversely, other components appear unaffected by hydrology or may be more strongly controlled by biotic interactions. This research, therefore, adds to understanding on microbial food web interactions in the context of flood and flow pulses in river-floodplain ecosystems.

Winter climate change affects growing-season soil microbial biomass and activity in northern hardwood forests

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Jorge Durán; Jennifer L. Morse; Peter M. Groffman; John L. Campbell; Lynn M. Christenson; Charles T. Driscoll; Timothy J. Fahey; Melany C. Fisk; Myron J. Mitchell; Pamela H. Templer

2014-01-01

Understanding the responses of terrestrial ecosystems to global change remains a major challenge of ecological research. We exploited a natural elevation gradient in a northern hardwood forest to determine how reductions in snow accumulation, expected with climate change, directly affect dynamics of soil winter frost, and indirectly soil microbial biomass and activity...

Microbial community dynamics of an urban drinking water distribution system subjected to phases of chloramination and chlorination treatments.

Science.gov (United States)

Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L; LeChevallier, Mark W; Liu, Wen-Tso

2012-11-01

Water utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population ≅ 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (chlorinated water, and Methylophilaceae, Methylococcaceae, and Pseudomonadaceae were more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (water and survived through the treatment process. Transient microbial populations including Flavobacteriaceae and Clostridiaceae were also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine.

Marine heatwaves and optimal temperatures for microbial assemblage activity.

Science.gov (United States)

Joint, Ian; Smale, Dan A

2017-02-01

The response of microbial assemblages to instantaneous temperature change was measured in a seasonal study of the coastal waters of the western English Channel. On 18 occasions between November 1999 and December 2000, bacterial abundance was assessed and temperature responses determined from the incorporation of 3 H leucine, measured in a temperature gradient from 5°C to 38°C. Q 10 values varied, being close to 2 in spring and summer but were >3 in autumn. There was a seasonal pattern in the assemblage optimum temperature (T opt ), which was out of phase with sea surface temperature. In July, highest 3 H-leucine incorporation rates were measured at temperatures that were only 2.8°C greater than ambient sea surface temperature but in winter, T opt was ∼20°C higher than the ambient sea surface temperature. Sea surface temperatures for the adjacent English Channel and Celtic Sea for 1982-2014 have periodically been >3°C higher than climatological mean temperatures. This suggests that discrete periods of anomalously high temperatures might be close to, or exceed, temperatures at which maximum microbial assemblage activity occurs. The frequency and magnitude of marine heatwaves are likely to increase as a consequence of anthropogenic climate change and extreme temperatures may influence the role of bacterial assemblages in biogeochemical processes. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Seasonal changes in nitrogen availability, and root and microbial uptake of ¹⁵N¹³C₉-phenylalanine and ¹⁵N-ammonium in situ at a temperate heath

DEFF Research Database (Denmark)

Andresen, Louise C.; Michelsen, Anders; Jonasson, Sven Evert

2011-01-01

In the plant biosynthesis of secondary compounds, phenylalanine is a precursor of condensed tannins. Tannins are deposited into the soil in plant root exudates and dead plant material and have been suggested to precipitate some soil nutrients and hence reduce nutrient availability for plants. Free...... amino acid,inorganic and microbial N concentration during the growing season was investigated in an ecosystem with a natural tannin chemosphere. The influence of tannins on the uptake of nitrogen in plants and microbes was followed by injecting tannic acid (TA), ammonium-15N and phenylalanine-15N/13C9...

Control of Pecan Weevil With Microbial Biopesticides.

Science.gov (United States)

Shapiro-Ilan, David I; Cottrell, Ted E; Bock, Clive; Mai, Kim; Boykin, Debbie; Wells, Lenny; Hudson, William G; Mizell, Russell F

2017-12-08

The pecan weevil, Curculio caryae (Horn) (Coleoptera: Curculionidae), is a key pest of pecans Carya illinoinensis ([Wangenh.] K. Koch) (Fagales: Juglandaceae). Control recommendations rely on broad spectrum chemical insecticides. Due to regulatory and environmental concerns, effective alternatives for C. caryae control must be sought for pecan production in conventional and organic systems. We explored the use of microbial biopesticides for control of C. caryae in Georgia pecan orchards. Three experiments were conducted. The first investigated an integrated microbial control approach in an organic system at two locations. Three microbial agents, Grandevo (based on byproducts of the bacterium Chromobacterium subtsugae Martin, Gundersen-Rindal, Blackburn & Buyer), the entomopathogenic nematode Steinernema carpocapsae (Weiser), and entomopathogenic fungus Beauveria bassiana (Balsamo) Vuillemin, were applied to each treatment plot (0.6 ha) at different times during the season. A second experiment compared the effects of S. carpocapsae and B. bassiana applied as single treatments relative to application of both agents (at different times); survival of C. caryae was assessed approximately 11 mo after larvae were added to pots sunk in an organic pecan orchard. In a conventional orchard (with 1.0 ha plots), the third experiment compared Grandevo applications to a commonly used regime of chemical insecticides (carbaryl alternated with a pyrethroid). All experiments were repeated in consecutive years. The combined pest management tactic (experiment 1) reduced C. caryae infestation relative to non-treated control plots in both locations in 2014 and one of the two locations in 2015 (the other location had less than 1% infestation). In experiment 2, no differences among combined microbial treatments, single-applied microbial treatments or different numbers of application were observed, yet all microbial treatments reduced C. caryae survival relative to the control. In the third

Microbial communities in riparian soils of a settling pond for mine drainage treatment.

Science.gov (United States)

Fan, Miaochun; Lin, Yanbing; Huo, Haibo; Liu, Yang; Zhao, Liang; Wang, Entao; Chen, Weimin; Wei, Gehong

2016-06-01

Mine drainage leads to serious contamination of soil. To assess the effects of mine drainage on microbial communities in riparian soils, we used an Illumina MiSeq platform to explore the soil microbial composition and diversity along a settling pond used for mine drainage treatment. Non-metric multidimensional scaling analysis showed that the microbial communities differed significantly among the four sampling zones (influent, upstream, downstream and effluent), but not seasonally. Constrained analysis of principal coordinates indicated heavy metals (zinc, lead and copper), total sulphur, pH and available potassium significantly influenced the microbial community compositions. Heavy metals were the key determinants separating the influent zone from the other three zones. Lower diversity indices were observed in the influent zone. However, more potential indicator species, related to sulphur and organic matter metabolism were found there, such as the sulphur-oxidizing genera Acidiferrobacter, Thermithiobacillus, Limnobacter, Thioprofundum and Thiovirga, and the sulphur-reducing genera Desulfotomaculum and Desulfobulbus; the organic matter degrading genera, Porphyrobacter and Paucimonas, were also identified. The results indicated that more microorganisms related to sulphur- and carbon-cycles may exist in soils heavily contaminated by mine drainage. Copyright © 2016 Elsevier Ltd. All rights reserved.

Rhizosphere effect of colonizer plant species on the development of soil microbial community during primary succession on postmining sites

Energy Technology Data Exchange (ETDEWEB)

Elhottova, D.; Kristufek, V.; Maly, S.; Frouz, J. [Academy of Sciences of the Czech Republic, Ceske Budejovice (Czech Republic). Inst. for Soil Biology

2009-07-01

The impact of pioneer plant species Tussilago farfara on structural, functional, and growth characterization of microbial community colonizing the spoil colliery substrate was studied in a laboratory microcosm experiment. Microcosms consisting of spoil substrate (0.7 dm{sup 3} of tertiary alkaline clay sediment from Sokolov brown-coal mine area) from a pioneer site (without vegetation, 5 years after heaping) were cultivated in a greenhouse with one plant of this species. Plant roots substantially increased microbial diversity and biomass after one season (7 months) of cultivation. Roots influenced the microbial community and had nearly twice the size, higher growth, and metabolic potential in comparison to the control. The development of microbial specialists improves the plant nutrient status. Bacterial nitrogen (N{sub 2}) fixators (Bradyrhizobium japonicum, Rhizobium radiobacter) and arbuscular mycorrhizal fungi were confirmed in the rhizosphere of Tussilago farfara.

Are variations in heterotrophic soil respiration related to changes in substrate availability and microbial biomass carbon in the subtropical forests?

Science.gov (United States)

Wei, Hui; Chen, Xiaomei; Xiao, Guoliang; Guenet, Bertrand; Vicca, Sara; Shen, Weijun

2015-12-16

Soil temperature and moisture are widely-recognized controlling factors on heterotrophic soil respiration (Rh), although they often explain only a portion of Rh variability. How other soil physicochemical and microbial properties may contribute to Rh variability has been less studied. We conducted field measurements on Rh half-monthly and associated soil properties monthly for two years in four subtropical forests of southern China to assess influences of carbon availability and microbial properties on Rh. Rh in coniferous forest was significantly lower than that in the other three broadleaf species-dominated forests and exhibited obvious seasonal variations in the four forests (P forests. The quantity and decomposability of dissolved organic carbon (DOC) were significantly important to Rh variations, but the effect of DOC content on Rh was confounded with temperature, as revealed by partial mantel test. Microbial biomass carbon (MBC) was significantly related to Rh variations across forests during the warm season (P = 0.043). Our results suggest that DOC and MBC may be important when predicting Rh under some conditions, and highlight the complexity by mutual effects of them with environmental factors on Rh variations.

Linking activity, composition and seasonal dynamics of atmospheric methane oxidizers in a meadow soil.

Science.gov (United States)

Shrestha, Pravin Malla; Kammann, Claudia; Lenhart, Katharina; Dam, Bomba; Liesack, Werner

2012-06-01

Microbial oxidation is the only biological sink for atmospheric methane. We assessed seasonal changes in atmospheric methane oxidation and the underlying methanotrophic communities in grassland near Giessen (Germany), along a soil moisture gradient. Soil samples were taken from the surface layer (0-10 cm) of three sites in August 2007, November 2007, February 2008 and May 2008. The sites showed seasonal differences in hydrological parameters. Net uptake rates varied seasonally between 0 and 70 μg CH(4) m(-2) h(-1). Greatest uptake rates coincided with lowest soil moisture in spring and summer. Over all sites and seasons, the methanotrophic communities were dominated by uncultivated methanotrophs. These formed a monophyletic cluster defined by the RA14, MHP and JR1 clades, referred to as upland soil cluster alphaproteobacteria (USCα)-like group. The copy numbers of pmoA genes ranged between 3.8 × 10(5)-1.9 × 10(6) copies g(-1) of soil. Temperature was positively correlated with CH(4) uptake rates (P50 vol% and primarily related to members of the MHP clade.

Seasonal Variation in Drinking and Domestic Water Sources and Quality in Port Harcourt, Nigeria

Science.gov (United States)

Kumpel, Emily; Cock-Esteb, Alicea; Duret, Michel; de Waal, Dominick; Khush, Ranjiv

2017-01-01

We compared dry and rainy season water sources and their quality in the urban region of Port Harcourt, Nigeria. Representative sampling indicated that municipal water supplies represent < 1% of the water sources. Residents rely on privately constructed and maintained boreholes that are supplemented by commercially packaged bottled and sachet drinking water. Contamination by thermotolerant coliforms increased from 21% of drinking water sources in the dry season to 42% of drinking water sources in the rainy season (N = 356 and N = 397). The most significant increase was in sachet water, which showed the lowest frequencies of contamination in the dry season compared with other sources (15%, N = 186) but the highest frequencies during the rainy season (59%, N = 76). Only half as many respondents reported drinking sachet water in the rainy season as in the dry season. Respondents primarily used flush or pour-flush toilets connected to septic tanks (85%, N = 399). The remainder relied on pit latrines and hanging (pier) latrines that drained into surface waters. We found significant associations between fecal contamination in boreholes and the nearby presence of hanging latrines. Sanitary surveys of boreholes showed that more than half were well-constructed, and we did not identify associations between structural or site deficiencies and microbial water quality. The deterioration of drinking water quality during the rainy season is a serious public health risk for both untreated groundwater and commercially packaged water, highlighting a need to address gaps in monitoring and quality control. PMID:27821689

Microbial community structures in algae cultivation ponds for bioconversion of agricultural wastes from livestock industry for feed production

Science.gov (United States)

Dynamics of seasonal microbial community compositions in algae cultivation ponds are complex. There is very limited knowledge on community compositions that may play significant roles in the bioconversion of manure nu¬trients to animal feed. Algae production is an alternative where land area for pro...

Microbial and environmental controls of methane fluxes along a soil moisture gradient in a Pacific coastal temperate rainforest

DEFF Research Database (Denmark)

Christiansen, Jesper Riis; Levy-Booth, David; Prescott, Cindy E.

2016-01-01

, and nutrient availability in three typical forest types across a soil moisture gradient. CH4 displayed a spatial variability changing from a net uptake in the upland soils (3.9–46 µmol CH4 m−2 h−1) to a net emission in the wetter soils (0–90 μmol CH4 m−2 h−1). Seasonal variations of CH4 fluxes were related......Most studies of greenhouse gas fluxes from forest soils in the coastal rainforest have considered carbon dioxide (CO2), whereas methane (CH4) has not received the same attention. Soil hydrology is a key driver of CH4 dynamics in ecosystems, but the impact on the function and distribution...... of the underlying microbial communities involved in CH4 cycling and the resultant net CH4 exchange is not well understood at this scale. We studied the growing season variations of in situ CH4 fluxes, microbial gene abundances of methanotrophs (CH4 oxidizers) and methanogens (CH4 producers), soil hydrology...

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

Energy Technology Data Exchange (ETDEWEB)

Graham, Emily B.; Crump, Alex R.; Resch, Charles T.; Fansler, Sarah; Arntzen, Evan; Kennedy, David W.; Fredrickson, Jim K.; Stegen, James C.

2016-12-16

Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptual model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.

Phosphorous fractions in soils of rubber-based agroforestry systems: Influence of season, management and stand age.

Science.gov (United States)

Liu, Chenggang; Jin, Yanqiang; Liu, Changan; Tang, Jianwei; Wang, Qingwei; Xu, Mingxi

2018-03-01

Rubber-based agroforestry system is a vital management practice and its productivity is often controlled by soil phosphorus (P) nutrient, but little information is available on P fractions dynamics in such system. The aim of this study was to examine the seasonal, management and stand age effects on P fractions, acid phosphatase activity, microbial biomass P, other physical-chemical properties and litter and roots in four systems: 10-year-old rubber mono- (YM) and intercropping (YI) with N-fixing species (NFS), 22-year-old mono- (MM) and intercropping (MI) in Xishuangbanna, Southwestern China. Most P fractions varied seasonally at different depths, with highest values in the fog-cool season (i.e. labile P at 5-60cm, non-labile P and total P at 30-60cm). By contrast, moderately labile P varied little over time, except in MI that had lower values in the rainy season. Compared with their monoculture counterparts, YI doubled resin-P i concentration but decreased NaHCO 3 -extractable P, HCl-P i and residual-P o at the 0-30cm depth, whereas MI had hardly any changes in P species at the 60-cm depth. Surprisingly, residual-P o was enriched down to the deepest soil (30-60cm) in both YI and MI in the fog-cool season. All P fractions, except NaOH 0.1 -P i , were greatly reduced with increasing stand age. In addition to plants uptake, these changes can be explained by seasonality in soil environments (e.g. moisture, temperature, pH and microbial activity) and decomposition of litter and roots. Moreover, YI decreased labile P o stock, but MI increased moderately labile P i at the 60-cm depth across seasons. The results imply that a large amount of residual-P o exists in acidic Oxisol from China and that they can be reasonably exploited to reduce the application of P fertilizers, highlighting the importance of P o pool. Taken together, intercropping mature rubber plantation with NFS appears to be an effective way to enhance productivity while maintaining adequate soil P

A wooded riparian strip set up for nitrogen removal can affect the water flux microbial composition

Directory of Open Access Journals (Sweden)

Mizanur Md. Rahman

2014-02-01

Full Text Available This research is part of a project aimed at verifying the potential of a specifically assessed wooded riparian zone in removing excess of combined nitrogen from the Zero river flow for the reduction of nutrient input into Venice Lagoon. Specific objectives were pursued to determine seasonal fluctuations of the microbial populations from the input water to a drainage ditch, conveying back the flux into the river after passing through the soil of the wooded riparian strip. The bacterial communities were determined by combined approaches involving cultivation, microscopic methods and DNA based techniques to determine both culturable and total microbial community in water. The results indicate that the size of the bacterial population, including the culturable fraction, increases from the river to the drainage ditch especially on the warm season. The multiple approach here adopted enabled also to demonstrate that the special condition created in the buffer strip supports the development and the metabolism of the microbial community. The nature of the bacterial population, in terms of phylotypes distribution, was investigated by 16S rDNA analysis indicating that the most represented genera belong to Gamma-proteobacteria, which is known to include an exceeding number of important pathogens. In spring, the effect of the buffer strip seems to significantly reduce such a sub-population. The changes observed for the total bacterial community composition become much evident in summer, as revealed by both denaturing gradient gel electrophoresis cluster analysis and by the diversity index calculation. The hydraulic management coupled to the suspension of farming practices and the development of the woody and herbaceous vegetation resulted in a condition suitable for the containment of undesired microbiota (mainly during the spring season while continuing to support denitrification activity (especially throughout the summer as verified by the total nitrogen

Engineering microbial cell factories for the production of plant natural products: from design principles to industrial-scale production.

Science.gov (United States)

Liu, Xiaonan; Ding, Wentao; Jiang, Huifeng

2017-07-19

Plant natural products (PNPs) are widely used as pharmaceuticals, nutraceuticals, seasonings, pigments, etc., with a huge commercial value on the global market. However, most of these PNPs are still being extracted from plants. A resource-conserving and environment-friendly synthesis route for PNPs that utilizes microbial cell factories has attracted increasing attention since the 1940s. However, at the present only a handful of PNPs are being produced by microbial cell factories at an industrial scale, and there are still many challenges in their large-scale application. One of the challenges is that most biosynthetic pathways of PNPs are still unknown, which largely limits the number of candidate PNPs for heterologous microbial production. Another challenge is that the metabolic fluxes toward the target products in microbial hosts are often hindered by poor precursor supply, low catalytic activity of enzymes and obstructed product transport. Consequently, despite intensive studies on the metabolic engineering of microbial hosts, the fermentation costs of most heterologously produced PNPs are still too high for industrial-scale production. In this paper, we review several aspects of PNP production in microbial cell factories, including important design principles and recent progress in pathway mining and metabolic engineering. In addition, implemented cases of industrial-scale production of PNPs in microbial cell factories are also highlighted.

Microbial based strategies for assessing rhizosphere-enhanced phytoremediation

Energy Technology Data Exchange (ETDEWEB)

Reynolds, C M [US Army Cold Regions Research and Engineering Lab., Hanover, NH (United States); Wolf, D C [Arkansas Univ., Fayetteville, AR (United States)

1999-01-01

The U.S. Department of Defense has considered phytoremediation to be a feasible technology to clean up contaminated sites in remote, cold regions. In cold regions, contaminated soil treatment rates are reduced by low temperatures and short treatment seasons. One technology that overcomes these limitations is rhizosphere-enhanced biotreatment which is a low-cost, simple technology that stimulates indigenous microorganisms. A study was conducted in which rhizosphere-enhanced treatment was compared to natural attenuation at a petroleum-contaminated site in Fairbanks, Alaska. The effects of vegetation and nutrient additions on remediation of soils contaminated with both diesel and crude oil were examined. Soil total petroleum hydrocarbon (TPH) concentrations in both treatments decreased relative to the initial TPH concentrations. After 640 days of treatment, the rhizosphere treatment had significantly lower TPH concentrations. It was concluded that an improved understanding of the time-dependent relationships between contaminant concentration changes and microbial community changes, along with improved techniques to characterize microbial communities, could provide a useful tool for monitoring the functioning of phytoremediation. 25 refs., 8 figs.

Microbial based strategies for assessing rhizosphere-enhanced phytoremediation

International Nuclear Information System (INIS)

Reynolds, C.M.; Wolf, D.C.

1999-01-01

The U.S. Department of Defense has considered phytoremediation to be a feasible technology to clean up contaminated sites in remote, cold regions. In cold regions, contaminated soil treatment rates are reduced by low temperatures and short treatment seasons. One technology that overcomes these limitations is rhizosphere-enhanced biotreatment which is a low-cost, simple technology that stimulates indigenous microorganisms. A study was conducted in which rhizosphere-enhanced treatment was compared to natural attenuation at a petroleum-contaminated site in Fairbanks, Alaska. The effects of vegetation and nutrient additions on remediation of soils contaminated with both diesel and crude oil were examined. Soil total petroleum hydrocarbon (TPH) concentrations in both treatments decreased relative to the initial TPH concentrations. After 640 days of treatment, the rhizosphere treatment had significantly lower TPH concentrations. It was concluded that an improved understanding of the time-dependent relationships between contaminant concentration changes and microbial community changes, along with improved techniques to characterize microbial communities, could provide a useful tool for monitoring the functioning of phytoremediation. 25 refs., 8 figs

How do microlocal environmental variations affect microbial activities of a Pinus halepensis litter in a Mediterranean coastal area?

Science.gov (United States)

Qasemian, Leila; Guiral, Daniel; Farnet, Anne-Marie

2014-10-15

Mediterranean coastal ecosystems suffer many different types of natural and anthropogenic environmental pressure. Microbial communities, major conductors of organic matter decomposition are also subject to these environmental constraints. In this study, our aim was to understand how microbial activities vary at a small spatio-temporal scale in a Mediterranean coastal environment. Microbial activities were monitored in a Pinus halepensis litter collected from two areas, one close to (10 m) and one far from (300 m) the French Mediterranean coast. Litters were transferred from one area to the other using litterbags and studied via different microbial indicators after 2, 5 and 13 months. Microbial Basal Respiration, qCO₂, certain enzyme activities (laccase, cellulase, β-glucosidase and acid phosphatase) and functional diversity via Biolog microplates were assayed in litterbags left in the area of origin as well as in litterbags transferred from one area to the other. Results highlight that microbial activities differ significantly in this short spatial scale over time. The influence of microlocal conditions more intensified for litters situated close to the sea, especially during summer seems to have a stressful effect on microbial communities, leading to less efficient functional activities. However, microbial activities were more strongly influenced by temporal variations linked to seasonality than by location. Copyright © 2014 Elsevier B.V. All rights reserved.

Cost of microbial larviciding for malaria control in rural Tanzania.

Science.gov (United States)

Rahman, Rifat; Lesser, Adriane; Mboera, Leonard; Kramer, Randall

2016-11-01

Microbial larviciding may be a potential supplement to conventional malaria vector control measures, but scant information on its relative implementation costs and effectiveness, especially in rural areas, is an impediment to expanding its uptake. We perform a costing analysis of a seasonal microbial larviciding programme in rural Tanzania. We evaluated the financial and economic costs from the perspective of the public provider of a 3-month, community-based larviciding intervention implemented in twelve villages in the Mvomero District of Tanzania in 2012-2013. Cost data were collected from financial reports and invoices and through discussion with programme administrators. Sensitivity analysis explored the robustness of our results to varying key parameters. Over the 2-year study period, approximately 6873 breeding sites were treated with larvicide. The average annual economic costs of the larviciding intervention in rural Tanzania are estimated at 2014 US$ 1.44 per person protected per year (pppy), US$ 6.18 per household and US$ 4481.88 per village, with the larvicide and staffing accounting for 14% and 58% of total costs, respectively. We found the costs pppy of implementing a seasonal larviciding programme in rural Tanzania to be comparable to the costs of other larviciding programmes in urban Tanzania and rural Kenya. Further research should evaluate the cost-effectiveness of larviciding relative to, and in combination with, other vector control strategies in rural settings. © 2016 John Wiley & Sons Ltd.

Effects of straw incorporation along with microbial inoculant on methane and nitrous oxide emissions from rice fields

Energy Technology Data Exchange (ETDEWEB)

Liu, Gang; Yu, Haiyang [State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Nanjing 210008 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Ma, Jing [State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Nanjing 210008 (China); Xu, Hua, E-mail: hxu@issas.ac.cn [State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Nanjing 210008 (China); Wu, Qinyan; Yang, Jinghui; Zhuang, Yiqing [Zhenjiang Institute of Agricultural Science of Hilly Regions in Jiangsu, Jurong 212400 (China)

2015-06-15

Incorporation of straw together with microbial inoculant (a microorganism agent, accelerating straw decomposition) is being increasingly adopted in rice cultivation, thus its effect on greenhouse gas (GHG) emissions merits serious attention. A 3-year field experiment was conducted from 2010 to 2012 to investigate combined effect of straw and microbial inoculant on methane (CH{sub 4}) and nitrous oxide (N{sub 2}O) emissions, global warming potential (GWP) and greenhouse gas intensity (GHGI) in a rice field in Jurong, Jiangsu Province, China. The experiment was designed to have treatment NPK (N, P and K fertilizers only), treatment NPKS (NPK plus wheat straw), treatment NPKSR (NPKS plus Ruilaite microbial inoculant) and treatment NPKSJ (NPKS plus Jinkuizi microbial inoculant). Results show that compared to NPK, NPKS increased seasonal CH{sub 4} emission by 280–1370%, while decreasing N{sub 2}O emission by 7–13%. When compared with NPKS, NPKSR and NPKSJ increased seasonal CH{sub 4} emission by 7–13% and 6–12%, respectively, whereas reduced N{sub 2}O emission by 10–27% and 9–24%, respectively. The higher CH{sub 4} emission could be attributed to the higher soil CH{sub 4} production potential triggered by the combined application of straw and microbial inoculant, and the lower N{sub 2}O emission to the decreased inorganic N content. As a whole, the benefit of lower N{sub 2}O emission was completely offset by increased CH{sub 4} emission, resulting in a higher GWP for NPKSR (5–12%) and NPKSJ (5–11%) relative to NPKS. Due to NPKSR and NPKSJ increased rice grain yield by 3–6% and 2–4% compared to NPKS, the GHGI values for NPKS, NPKSR and NPKSJ were comparable. These findings suggest that incorporating straw together with microbial inoculant would not influence the radiative forcing of rice production in the terms of per unit of rice grain yield relative to the incorporation of straw alone. - Highlights: • This paper presents 3-year measurements of CH

The Rhizosphere Zone: A Hot Spot of Microbial Activity and Methylmercury Production in Saltmarsh Sediments of San Francisco Bay, California

Science.gov (United States)

Windham-Myers, L.; Marvin-Dipasquale, M.; Voytek, M.; Kirshtein, J.; Krabbenhoft, D. P.; Agee, J. L.; Cox, M.; Kakouros, E.; Collins, J. N.; Yee, D.

2008-12-01

Tidal marshes of varying hydrology and salinity have been shown to have high rates of microbial methylmercury (MeHg) production, especially the periodically flooded, higher elevations which are densely vegetated with shallowly rooted plants. The specific influence of emergent wetland plants and their active rhizosphere (root zone) on mercury (Hg) biogeochemistry, however, is poorly understood. Seasonal and spatial patterns of Hg biogeochemistry were examined in 2005 and 2006 at three marshes along a salinity gradient of the Petaluma River, in Northern San Francisco Bay, California. In addition, to directly examine the influence of rhizosphere activity on MeHg production, a suite of devegetation experiments was conducted in 2006 within each marsh using paired vegetated and devegetated plots in two marsh subhabitats: poorly- drained interior sites and well-drained "edge" sites near slough channels. Surface sediment (0-2cm) was sampled in both April and August from these plots, as well as from 1st and 3rd order slough channels that were naturally free of vegetation. Vegetated marsh sites produced 3- to19-fold more MeHg than did slough sites, and MeHg production rates were greater in marsh interior sites compared to more oxic marsh "edge" sites. Microbial biomass (ng DNA gdrysed) was greater in vegetated marsh settings, compared to slough channels, and increased significantly between April and August at all marsh sites. Despite this seasonal increase in microbial biomass, MeHg concentrations and production rates decreased from April to August in vegetated surface sediments. Microbial indicators of methylation also decreased from April to August, including rates of microbial sulfate reduction and the abundance of iron- and sulfate- reducing bacterial DNA. Results from the devegetated plots suggest that root exudation of fermentative labile carbon to surface soils is responsible for the higher microbial biomass, and the higher relative abundance of iron- and sulfate

Applicability of API ZYM to capture seasonal and spatial variabilities in lake and river sediments.

Science.gov (United States)

Patel, Drashti; Gismondi, Renee; Alsaffar, Ali; Tiquia-Arashiro, Sonia M

2018-05-02

Waters draining into a lake carry with them much of the suspended sediment that is transported by rivers and streams from the local drainage basin. The organic matter processing in the sediments is executed by heterotrophic microbial communities, whose activities may vary spatially and temporally. Thus, to capture and evaluate some of these variabilities in the sediments, we sampled six sites: three from the St. Clair River and three from Lake St. Clair in spring, summer, fall, and winter of 2016. At all sites and dates, we investigated the spatial and temporal variations in 19 extracellular enzyme activities using API ZYM. Our results indicated that a broad range of enzymes were found to be active in the sediments. Phosphatases, lipases, and esterases were synthesized most intensively by the sediment microbial communities. No consistent difference was found between the lake and sediment samples. Differences were more obvious between sites and seasons. Sites with the highest metabolic (enzyme) diversity reflected the capacity of the sediment microbial communities to breakdown a broader range of substrates and may be linked to differences in river and lake water quality. The seasonal variability of the enzymes activities was governed by the variations of environmental factors caused by anthropogenic and terrestrial inputs, and provides information for a better understanding of the dynamics of sediment organic matter of the river and lake ecosystems. The experimental results suggest that API ZYM is a simple and rapid enzyme assay procedure to evaluate natural processes in ecosystems and their changes.

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

Science.gov (United States)

Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

2016-11-01

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

Cultivation-dependent analysis of the microbial diversity associated with the seagrass meadows in Xincun Bay, South China Sea.

Science.gov (United States)

Jiang, Yu-Feng; Ling, Juan; Wang, You-Shao; Chen, Biao; Zhang, Yan-Ying; Dong, Jun-De

2015-10-01

Microbial communities have largely existed in the seagrass meadows. A total of 496 strains of the bacteria in the seagrass meadows, which belonged to 50 genera, were obtained by the plate cultivation method from three sites of Xincun Bay, South China Sea. The results showed that Bacillales and Vibrionales accounted for the highest proportions of organisms in all communities. The diversity of the bacteria in the sediment was higher than that associated with seagrass. Thalassia hemperichii possessed the highest abundance of bacteria, followed by Enhalus acoroides and Cymodocea rotundata. Robust seasonal dynamics in microbial community composition were also observed. It was found that microbial activities were closely tied to the growth stage of the seagrass. The microbial distribution was the lowest in site 3. The abundance of the bacteria was linked to the interactions between bacteria and plants, the condition of plant and even the coastal water quality and the nutrition level in the sediment.

NEW SEASON NEW HOPES: OFF-SEASON OPTIMISM

Directory of Open Access Journals (Sweden)

Oguz Ersan

2017-12-01

Full Text Available While literature on the relation between on-field sports performance and stock returns is ample, there is very limited evidence on off-season stage. Constituting around 3 months, off-seasons do not only occupy a significant part of the year but also represent totally different characteristics than on-seasons. They lack the periodic, unambiguous news events in on-seasons (match results, instead they are associated with highly uncertain transfer news and rumors. We show that this distinction has several impacts on the stock market performances of soccer clubs. Most notably, off-seasons generate substantially higher (excess returns. After controlling for other variables, the estimated effect of off-season periods is as high as 38.75%, annually. In line with several seminal studies, we link this fact to increased optimism and betting behavior through uncertain periods; and periods prior to the start of a new calendar (in our case, new season. For all of the examined 7 clubs (3 from Italy and 4 from Turkey, mean excess returns over the market are positive (negative in off-seasons (on-seasons. On-seasons are associated with increased trading activity due to more frequent news. Stocks of Italian clubs are evidently more volatile through off-seasons while volatility results for the stocks of Turkish clubs are not consistent.

Microbial community analysis of fouled reverse osmosis membranes used in water recycling

KAUST Repository

Ayache, C.; Manes, Carmem Lara De O; Pidou, Marc; Croue, Jean-Philippe; Gernjak, Wolfgang

2013-01-01

Biofouling on RO membranes has major cost implications in water reclamation. In this study membranes and water samples were collected from a RO pilot-plant operated on two sites to study the differences in microbial communities in order to develop a better understanding of the biofouling. For the two sites studied, the examination of the front membrane of the first stage and the tail membrane of the second stage of the RO train using 16S rRNA gene-based molecular technique showed that bacteria were similar on both stages and no significant effect of the membrane location within the RO train on the biofilm development could be discerned. However, the comparison of the identified bacteria from membrane samples between the two sites showed that each site is specific, leading to a different composition of microbial communities. The different nutrient concentrations in the RO feed water due to the different biological pre-treatments are one potential explanation for the observed differences in the microbial communities. Seasonal variations also play a major role in the development of microbial communities as shown by the significant differences observed between the communities measured in the samples in winter and summer on the second site. The results did not show similarity between the species identified on the RO membranes and in the feed water. Hence, the relationship of microbial community between the water generated during the pre-treatment process and RO membranes is not obvious. From this study, results showed that there is an actual need to investigate the development of microbial communities on membrane surface in real conditions in order to suggest tailored solutions for biofouling control and removal. © 2013 Elsevier Ltd.

Microbial community analysis of fouled reverse osmosis membranes used in water recycling

KAUST Repository

Ayache, C.

2013-06-01

Biofouling on RO membranes has major cost implications in water reclamation. In this study membranes and water samples were collected from a RO pilot-plant operated on two sites to study the differences in microbial communities in order to develop a better understanding of the biofouling. For the two sites studied, the examination of the front membrane of the first stage and the tail membrane of the second stage of the RO train using 16S rRNA gene-based molecular technique showed that bacteria were similar on both stages and no significant effect of the membrane location within the RO train on the biofilm development could be discerned. However, the comparison of the identified bacteria from membrane samples between the two sites showed that each site is specific, leading to a different composition of microbial communities. The different nutrient concentrations in the RO feed water due to the different biological pre-treatments are one potential explanation for the observed differences in the microbial communities. Seasonal variations also play a major role in the development of microbial communities as shown by the significant differences observed between the communities measured in the samples in winter and summer on the second site. The results did not show similarity between the species identified on the RO membranes and in the feed water. Hence, the relationship of microbial community between the water generated during the pre-treatment process and RO membranes is not obvious. From this study, results showed that there is an actual need to investigate the development of microbial communities on membrane surface in real conditions in order to suggest tailored solutions for biofouling control and removal. © 2013 Elsevier Ltd.

Influenza Seasonal Summary, 2014-2015 Season

Science.gov (United States)

2015-08-14

Influenza Seasonal Summarv 2014-2015 Season EpiData Center Department Communicable Disease Division NMCPHC-EDC-TR-394-2015 REPORT DOCUMENTATION... Influenza Seasonal Summary, 2014-2015 Season Sb. GRANT NUMBER $c. PROGRAM ELEMENT NUMBER 6. AUTHORjS) Sd. PROJECT NUMBER Ashleigh K McCabe, Kristen R...SUPPLEMENTARY NOTES 1<l. ABSTRACT This report summartzes influenza activity among Department of Navy (DON) and Depar1ment of Defense (DOD

Predicting the microbial exposure risks in urban floods using GIS, building simulation, and microbial models.

Science.gov (United States)

Taylor, Jonathon; Biddulph, Phillip; Davies, Michael; Lai, Ka man

2013-01-01

London is expected to experience more frequent periods of intense rainfall and tidal surges, leading to an increase in the risk of flooding. Damp and flooded dwellings can support microbial growth, including mould, bacteria, and protozoa, as well as persistence of flood-borne microorganisms. The amount of time flooded dwellings remain damp will depend on the duration and height of the flood, the contents of the flood water, the drying conditions, and the building construction, leading to particular properties and property types being prone to lingering damp and human pathogen growth or persistence. The impact of flooding on buildings can be simulated using Heat Air and Moisture (HAM) models of varying complexity in order to understand how water can be absorbed and dry out of the building structure. This paper describes the simulation of the drying of building archetypes representative of the English building stock using the EnergyPlus based tool 'UCL-HAMT' in order to determine the drying rates of different abandoned structures flooded to different heights and during different seasons. The results are mapped out using GIS in order to estimate the spatial risk across London in terms of comparative flood vulnerability, as well as for specific flood events. Areas of South and East London were found to be particularly vulnerable to long-term microbial exposure following major flood events. Copyright © 2012 Elsevier Ltd. All rights reserved.

Functional response of a near-surface soil microbial community to a simulated underground CO2 storage leak.

Science.gov (United States)

Morales, Sergio E; Holben, William E

2013-01-01

Understanding the impacts of leaks from geologic carbon sequestration, also known as carbon capture and storage, is key to developing effective strategies for carbon dioxide (CO2) emissions management and mitigation of potential negative effects. Here, we provide the first report on the potential effects of leaks from carbon capture and storage sites on microbial functional groups in surface and near-surface soils. Using a simulated subsurface CO2 storage leak scenario, we demonstrate how CO2 flow upward through the soil column altered both the abundance (DNA) and activity (mRNA) of microbial functional groups mediating carbon and nitrogen transformations. These microbial responses were found to be seasonally dependent and correlated to shifts in atmospheric conditions. While both DNA and mRNA levels were affected by elevated CO2, they did not react equally, suggesting two separate mechanisms for soil microbial community response to high CO2 levels. The results did not always agree with previous studies on elevated atmospheric (rather than subsurface) CO2 using FACE (Free-Air CO2 Enrichment) systems, suggesting that microbial community response to CO2 seepage from the subsurface might differ from its response to atmospheric CO2 increases.

Alterações microbianas no solo durante o ciclo do milho nos sistemas plantio direto e convencional Microbial changes in soil during a maize crop season in no-till and conventional systems

Directory of Open Access Journals (Sweden)

Luciano Kayser Vargas

2004-08-01

Full Text Available A disponibilidade de resíduos de aveia-preta, com relação C:N elevada, resulta em imobilização microbiana de nitrogênio no solo, exigindo cuidados no manejo da adubação nitrogenada da cultura subseqüente. O objetivo deste trabalho foi avaliar as alterações na estrutura da comunidade microbiana ao longo do ciclo do milho, na presença de resíduos de aveia-preta e da aplicação de nitrogênio. Foram coletadas amostras de um Argissolo Vermelho distrófico no dia da semeadura do milho e 46, 62, 88 e 112 dias após a semeadura. O nitrogênio foi aplicado 25 dias e 49 dias após a semeadura. As alterações na comunidade microbiana foram avaliadas mediante relações entre carbono (C e nitrogênio (N, nitrogênio reativo com ninidrina (N-Nin e carboidratos (CHO da biomassa microbiana, além da análise do rDNA fúngico e bacteriano. As diferenças na composição da comunidade microbiana, reveladas pela análise do rDNA, relacionaram-se mais com as relações C:N e C:N-Nin do que com a relação C:CHO. As relações C:N-Nin e C:N e as avaliações do rDNA mostraram um predomínio inicial de população fúngica. Com a aplicação de N, a população bacteriana tornou-se preponderante e, ao final do ciclo do milho, retornou para uma condição semelhante à inicial.The availability of black oat residues, with high C:N ratio, leads to microbial immobilization of soil nitrogen, demanding special strategies to supply nitrogen to subsequent crops. The objective of this work was to evaluate shifts in microbial community structure due to the availability of black oat residues and nitrogen applications during the corn growing season. Soil (Paleudult samples were collected on the day of the corn seeding and after 46, 62, 88 and 112 days. Nitrogen fertilizer was applied 25 and 49 days after corn seeding. Changes in microbial community were assessed by microbial biomass carbon (C and nitrogen (N, ninhydrin-reactive N (N-Nin and carbohydrates (CHO

Rhizobial inoculation increases soil microbial functioning and gum arabic production of 13-years old Senegalia senegal (L. Britton, trees in the North part of Senegal

Directory of Open Access Journals (Sweden)

Dioumacor FALL

2016-09-01

Full Text Available Abstract Rhizobial inoculation has been widely used in controlled conditions as a substitute for chemical fertilizers to increase plants growth and productivity. However, very little is known about such effects on mature trees in natural habitats. In this study, we investigated the effect of rhizobial inoculation on soil total microbial biomass, mineral nitrogen content, potential CO2 respiration, fluorescein diacetate (FDA, acid phosphatase activities and gum arabic production by 13-years old Senegalia senegal (Syn. Acacia senegal under natural conditions in the north part of Senegal during two consecutive years. Rhizobial inoculation was performed at the beginning of the rainy season (July for both years with a cocktail of four strains (CIRADF 300, CIRADF 301, CIRADF 302 and CIRADF 303. Rhizospheric soils were collected in both dry and rainy seasons to a depth of 0-25 cm under uninoculated (UIN and inoculated (IN trees. Trees were tapped in November (beginning of dry season using traditional tools. Gum arabic was harvested every 15 days from December to March. The results obtained from both years demonstrated that rhizobial inoculation increased significantly the percentage of trees producing gum arabic, gum arabic production per tree, soil microbial biomass, FDA and acid phosphatase activities. However, there was no significant effect on C mineralization and mineral nitrogen (N content. Gum arabic production was positively correlated to rainfall, soil microbial biomass and mineral nitrogen content. Our results showed a positive effect of rhizobial inoculation on soil microbial functioning and gum arabic production by mature S. senegal trees. These important findings deserve to be conducted in several contrasting sites in order to improve gum arabic production and contribute to increase rural population incomes.

Rhizobial Inoculation Increases Soil Microbial Functioning and Gum Arabic Production of 13-Year-Old Senegalia senegal (L.) Britton, Trees in the North Part of Senegal.

Science.gov (United States)

Fall, Dioumacor; Bakhoum, Niokhor; Nourou Sall, Saïdou; Zoubeirou, Alzouma Mayaki; Sylla, Samba N; Diouf, Diegane

2016-01-01

Rhizobial inoculation has been widely used in controlled conditions as a substitute for chemical fertilizers to increase plants growth and productivity. However, very little is known about such effects on mature trees in natural habitats. In this study, we investigated the effect of rhizobial inoculation on soil total microbial biomass, mineral nitrogen content, potential CO2 respiration, fluorescein diacetate (FDA), acid phosphatase activities, and gum arabic production by 13-year-old Senegalia senegal (synonym: Acacia senegal) under natural conditions in the north part of Senegal during two consecutive years. Rhizobial inoculation was performed at the beginning of the rainy season (July) for both years with a cocktail of four strains (CIRADF 300, CIRADF 301, CIRADF 302, and CIRADF 303). Rhizospheric soils were collected in both dry and rainy seasons to a depth of 0-25 cm under uninoculated and inoculated trees. Trees were tapped in November (beginning of dry season) using traditional tools. Gum arabic was harvested every 15 days from December to March. The results obtained from both years demonstrated that rhizobial inoculation increased significantly the percentage of trees producing gum arabic, gum arabic production per tree, soil microbial biomass, FDA, and acid phosphatase activities. However, there was no significant effect on C mineralization and mineral nitrogen (N) content. Gum arabic production was positively correlated to rainfall, soil microbial biomass, and mineral nitrogen content. Our results showed a positive effect of rhizobial inoculation on soil microbial functioning and gum arabic production by mature S. senegal trees. These important findings deserve to be conducted in several contrasting sites in order to improve gum arabic production and contribute to increase rural population incomes.

Differential sensitivity of total and active soil microbial communities to drought and forest management.

Science.gov (United States)

Bastida, Felipe; Torres, Irene F; Andrés-Abellán, Manuela; Baldrian, Petr; López-Mondéjar, Rubén; Větrovský, Tomáš; Richnow, Hans H; Starke, Robert; Ondoño, Sara; García, Carlos; López-Serrano, Francisco R; Jehmlich, Nico

2017-10-01

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial

Seasonal patterns in immune indices reflect microbial loads on birds but not microbes in the wider environment

NARCIS (Netherlands)

Horrocks, N.P.C.; Matson, K.D.; Shobrak, M.; Tinbergen, J.M.; Tieleman, B.I.

2012-01-01

Documenting patterns in immune function is a first step to understanding immune variation, but to comprehend causes and consequences, antigen and parasite exposure that may drive such variation must be determined. We measured host-independent microbial exposure in five species of larks (Alaudidae)

Linking activity, composition and seasonal dynamics of atmospheric methane oxidizers in a meadow soil

Science.gov (United States)

Shrestha, Pravin Malla; Kammann, Claudia; Lenhart, Katharina; Dam, Bomba; Liesack, Werner

2012-01-01

Microbial oxidation is the only biological sink for atmospheric methane. We assessed seasonal changes in atmospheric methane oxidation and the underlying methanotrophic communities in grassland near Giessen (Germany), along a soil moisture gradient. Soil samples were taken from the surface layer (0–10 cm) of three sites in August 2007, November 2007, February 2008 and May 2008. The sites showed seasonal differences in hydrological parameters. Net uptake rates varied seasonally between 0 and 70 μg CH4 m−2 h−1. Greatest uptake rates coincided with lowest soil moisture in spring and summer. Over all sites and seasons, the methanotrophic communities were dominated by uncultivated methanotrophs. These formed a monophyletic cluster defined by the RA14, MHP and JR1 clades, referred to as upland soil cluster alphaproteobacteria (USCα)-like group. The copy numbers of pmoA genes ranged between 3.8 × 105–1.9 × 106 copies g−1 of soil. Temperature was positively correlated with CH4 uptake rates (P50 vol% and primarily related to members of the MHP clade. PMID:22189499

Influence of prevailing disturbances on soil biology and biochemistry of montane habitats at Nanda Devi Biosphere Reserve, India during wet and dry seasons

DEFF Research Database (Denmark)

Singh, S.K.; Singh, Anoop; Rai, J.P.N.

2011-01-01

The impact of prevailing disturbances in montane habitats of Nanda Devi Biosphere Reserve (NDBR) was studied on soil microbial population, biomass, soil respiration and enzyme activities during wet and dry seasons. The physico-chemical characteristics of soils exhibited conspicuous variation in t...

Impact of long term pesticide usage on soil microbial activities and 14C-monocrotophos degradation

International Nuclear Information System (INIS)

Tayaputch, N.; Pimpan, P.; Phaikaew, Y.; Chukiatwatana, L.

2001-01-01

The effects of long term pesticide usage on soil microbial activities and degradation of 14 C-monocrotophos was observed under cotton field conditions. The experimental field was divided into treated and untreated plots. Pesticides were applied to treated plots at weekly intervals as in common practice in Thailand. The total numbers of applications were 11, 16 and 16 for first, second and third crop seasons, during the three years from 1996 to 1998. Soil samples at depths of 0-15 cm and 15-30 cm were sampled before and after pesticide application for the first two crops, while in the third crop season only the surface layer of soil was taken. The samples were assessed for CO 2 from respiration, soil microbial population, iron reduction capacity, and rates of nitrification. Soil biomass and microbial activities as measured from respiration and iron reduction decreased in the treated plots at both depths after each pesticide application over the three crop seasons, whereas samples from untreated plots at both depths did not show decreases. Repeated application of pesticides did not show any effect on nitrification rates of the first crop but there was inhibition in the second and third crops. Soil columns, treated with 14 C-monocrotophos one week after last pesticide application, were harvested after 0, 3, 6, 9, 18, 24 and 30 months. Extractable residues of 14 C were found only in the 0-15 cm layer. In treated and untreated plots, residues declined from 80.17 and 85.68 to 0.44% of the applied 14 C within 6 months. The long term usage of pesticides did not affect the half-life of 14 C-monocrotophos. Bound residues of 14 C were found at the highest concentrations, 18.94 and 12.58% of that applied, at 6 months in treated and untreated plots, thereafter the binding decreased to 4.68 and 2.74% within 30 months. (author)

Effects of fire on soil nitrogen dynamics and microbial biomass in savannas of Central Brazil

Directory of Open Access Journals (Sweden)

Nardoto Gabriela Bielefeld

2003-01-01

Full Text Available The objective of this work was to study the effects of fire on net N mineralization and soil microbial biomass in burned and unburned cerrado stricto sensu sites. The study was carried out from April 1998 to April 2000. The pH values were significantly higher in the burned site while soil moisture content was significantly higher in the unburned site (P<0.05. The soil C/N ratio was 22/1 and the available NO3-N ranged between 1.5 and 2.8 mg kg-¹ dry weight. However, the NH4-N concentration ranged between 3 and 34 mg kg-1 dry weight in the burned site and between 3 and 22 mg kg-1 dry weight in the unburned site. The NH4-N increased after fire, but no significant changes were observed for NO3-N (P<0.05. The NO3-N accumulation occurred in short periods during the rainy season. The rates of net N mineralization increased during the rainy season while reductions in soil microbial biomass were observed at both sites. This suggested that the peak in microbial activities occurred with the first rain events, with an initial net immobilization followed by net mineralization. Both sites presented the same pattern for mineralization/immobilization, however, the amount of inorganic-N cycled annually in unburned site was 14.7 kg ha-1 per year while the burned site presented only 3.8 kg ha-¹ of inorganic-N, one year after the burning.

Microbial ecology-based engineering of Microbial Electrochemical Technologies.

Science.gov (United States)

Koch, Christin; Korth, Benjamin; Harnisch, Falk

2018-01-01

Microbial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge-driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Drift in ocean currents impacts intergenerational microbial exposure to temperature.

Science.gov (United States)

Doblin, Martina A; van Sebille, Erik

2016-05-17

Microbes are the foundation of marine ecosystems [Falkowski PG, Fenchel T, Delong EF (2008) Science 320(5879):1034-1039]. Until now, the analytical framework for understanding the implications of ocean warming on microbes has not considered thermal exposure during transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Here we show that upper-ocean microbes experience along-trajectory temperature variability up to 10 °C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents can increase the thermal exposure of microbes and suggests that microbial populations with broad thermal tolerance will survive transport to distant regions of the ocean and invade new habitats. Our findings also suggest that advection has the capacity to influence microbial community assemblies, such that regions with strong currents and large thermal fluctuations select for communities with greatest plasticity and evolvability, and communities with narrow thermal performance are found where ocean currents are weak or along-trajectory temperature variation is low. Given that fluctuating environments select for individual plasticity in microbial lineages, and that physiological plasticity of ancestors can predict the magnitude of evolutionary responses of subsequent generations to environmental change [Schaum CE, Collins S (2014) Proc Biol Soc 281(1793):20141486], our findings suggest that microbial populations in the sub-Antarctic (∼40°S), North Pacific, and North Atlantic will have the most capacity to adapt to contemporary ocean warming.

Microbial bebop: creating music from complex dynamics in microbial ecology.

Science.gov (United States)

Larsen, Peter; Gilbert, Jack

2013-01-01

In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams.

Science.gov (United States)

Milan, M; Carraro, L; Fariselli, P; Martino, M E; Cavalieri, D; Vitali, F; Boffo, L; Patarnello, T; Bargelloni, L; Cardazzo, B

2018-01-01

Given the crucial role of microbiota in host development, health, and environmental interactions, genomic analyses focusing on host-microbiota interactions should certainly be considered in the investigation of the adaptive mechanisms to environmental stress. Recently, several studies suggested that microbiota associated to digestive tract is a key, although still not fully understood, player that must be considered to assess the toxicity of environmental contaminants. Bacteria-dependent metabolism of xenobiotics may indeed modulate the host toxicity. Conversely, environmental variables (including pollution) may alter the microbial community and/or its metabolic activity leading to host physiological alterations that may contribute to their toxicity. Here, 16s rRNA gene amplicon sequencing has been applied to characterize the hepatopancreas microbiota composition of the Manila clam, Ruditapes philippinarum. The animals were collected in the Venice lagoon area, which is subject to different anthropogenic pressures, mainly represented by the industrial activities of Porto Marghera (PM). Seasonal and geographic differences in clam microbiotas were explored and linked to host response to chemical stress identified in a previous study at the transcriptome level, establishing potential interactions among hosts, microbes, and environmental parameters. The obtained results showed the recurrent presence of putatively detoxifying bacterial taxa in PM clams during winter and over-representation of several metabolic pathways involved in xenobiotic degradation, which suggested the potential for host-microbial synergistic detoxifying actions. Strong interaction between seasonal and chemically-induced responses was also observed, which partially obscured such potentially synergistic actions. Seasonal variables and exposure to toxicants were therefore shown to interact and substantially affect clam microbiota, which appeared to mirror host response to environmental variation. It

Microbial nitrogen transformation potential in surface run-off leachate from a tropical landfill

International Nuclear Information System (INIS)

Mangimbulude, Jubhar C.; Straalen, Nico M. van; Röling, Wilfred F.M.

2012-01-01

Highlights: ► Microbial nitrogen transformations can alleviate toxic ammonium discharge. ► Aerobic ammonium oxidation was rate-limiting in Indonesian landfill leachate. ►Organic nitrogen ammonification was most dominant. ► Anaerobic nitrate reduction and ammonium oxidation potential were also high. ► A two-stage aerobic-anaerobic nitrogen removal system needs to be implemented. - Abstract: Ammonium is one of the major toxic compounds and a critical long-term pollutant in landfill leachate. Leachate from the Jatibarang landfill in Semarang, Indonesia, contains ammonium in concentrations ranging from 376 to 929 mg N L −1 . The objective of this study was to determine seasonal variation in the potential for organic nitrogen ammonification, aerobic nitrification, anaerobic nitrate reduction and anaerobic ammonium oxidation (anammox) at this landfilling site. Seasonal samples from leachate collection treatment ponds were used as an inoculum to feed synthetic media to determine potential rates of nitrogen transformations. Aerobic ammonium oxidation potential ( −1 h −1 ) was more than a hundred times lower than the anaerobic nitrogen transformation processes and organic nitrogen ammonification, which were of the same order of magnitude. Anaerobic nitrate oxidation did not proceed beyond nitrite; isolates grown with nitrate as electron acceptor did not degrade nitrite further. Effects of season were only observed for aerobic nitrification and anammox, and were relatively minor: rates were up to three times higher in the dry season. To completely remove the excess ammonium from the leachate, we propose a two-stage treatment system to be implemented. Aeration in the first leachate pond would strongly contribute to aerobic ammonium oxidation to nitrate by providing the currently missing oxygen in the anaerobic leachate and allowing for the growth of ammonium oxidisers. In the second pond the remaining ammonium and produced nitrate can be converted by a

[Influence of Mirabilis jalapa Linn. Growth on the Microbial Community and Petroleum Hydrocarbon Degradation in Petroleum Contaminated Saline-alkali Soil].

Science.gov (United States)

Jiao, Hai-hua; Cui, Bing-jian; Wu, Shang-hua; Bai, Zhi-hui; Huang, Zhan-bin

2015-09-01

In order to explore the effect of Mirabilis jalapa Linn. growth on the structure characteristics of the microbial community and the degradation of petroleum hydrocarbon (TPH) in the petroleum-contaminated saline-alkali soil, Microbial biomass and species in the rhizosphere soils of Mirabilis jalapa Linn. in the contaminated saline soil were studied with the technology of phospholipid fatty acids (PLFAs) analysis. The results showed that comparing to CK soils without Mirabilis jalapa Linn., the ratio of PLFAs species varied were 71. 4%, 69. 2% and 33. 3% in the spring, summer and autumn season, respectively. In addition, there was distinct difference of the biomasses of the microbial community between the CK and rhizosphere soils and among the difference seasons of growth of Mirabilis jalapa Linn.. Compare to CK soil, the degradation rates of total petroleum hydrocarbon (TPH) was increased by 47. 6%, 28. 3%, and 18. 9% in spring, summer, and autumn rhizosphere soils, respectively. Correlation analysis was used to determine the correlation between TPH degradation and the soil microbial community. 77. 8% of the total soil microbial PLFAs species showed positive correlation to the TPH degradation (the correlation coefficient r > 0), among which, 55. 6% of PLFAs species showed high positive correlation(the correlation coefficient was r≥0. 8). In addition, the relative content of SAT and MONO had high correlation with TPH degradation in the CK sample soils, the corelation coefficient were 0. 92 and 0. 60 respectively; However, the percent of positive correlation was 42. 1% in the rhizosphere soils with 21. 1% of them had high positive correlation. The relative content of TBSAT, MONO and CYCLO had moderate or low correlation in rhizosphere soils, and the correlation coefficient were 0. 56, 0. 50, and 0. 07 respectively. Our study showed that the growth of mirabilis Mirabilis jalapa Linn. had a higher influence on the species and biomass of microbial community in the

Antimicrobial susceptibility and Ribosomal-RNA gene restriction patterns among Staphylococcus-intermedius from healthy dogs and from dogs sufferning from pyoderma or otitis-externa

DEFF Research Database (Denmark)

Pedersen, Karl; Wegener, Henrik Caspar

1995-01-01

A total of 60 Staphlococcus intermedius strains from dogs were investigated by their sensitivity to various antibiotics (50 strains) and by their rRNA gene restriction patterns (ribotyping) (60 strains). Fifteen isolates were from healthy dogs, 9 with otitis externa, and 36 with pyoderma, including......, enrofloxacin, and sulphonamides with trimethoprim. There were no significant differences in antimicrobial susceptibility patterns observed among isolates from pyoderma, otitis externa or healthy dogs. Among the 60 strains studied by ribotyping, 10 different ribotypes were identified: 6 different ribotypes...... among isolates from otitis externa, 8 among isolates from pyoderma, and 5 among isolates from healthy dogs. One ribotype (profile C) was dominant among the isolates from healthy dogs while another ribotype (profile A) was dominant among strains from dogs suffering from pyoderma. This profile...

Microbial bebop: creating music from complex dynamics in microbial ecology.

Directory of Open Access Journals (Sweden)

Peter Larsen

Full Text Available In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm. from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

The Influence of Ecological and Conventional Plant Production Systems on Soil Microbial Quality under Hops (Humulus lupulus)

Science.gov (United States)

Oszust, Karolina; Frąc, Magdalena; Gryta, Agata; Bilińska, Nina

2014-01-01

The knowledge about microorganisms—activity and diversity under hop production is still limited. We assumed that, different systems of hop production (within the same soil and climatic conditions) significantly influence on the composition of soil microbial populations and its functional activity (metabolic potential). Therefore, we compared a set of soil microbial properties in the field experiment of two hop production systems (a) ecological based on the use of probiotic preparations and organic fertilization (b) conventional—with the use of chemical pesticides and mineral fertilizers. Soil analyses included following microbial properties: The total number microorganisms, a bunch of soil enzyme activities, the catabolic potential was also assessed following Biolog EcoPlates®. Moreover, the abundance of ammonia-oxidizing archaea (AOA) was characterized by terminal restriction fragment length polymorphism analysis (T-RFLP) of PCR ammonia monooxygenase α-subunit (amoA) gene products. Conventional and ecological systems of hop production were able to affect soil microbial state in different seasonal manner. Favorable effect on soil microbial activity met under ecological, was more probably due to livestock-based manure and fermented plant extracts application. No negative influence on conventional hopyard soil was revealed. Both type of production fulfilled fertilizing demands. Under ecological production it was due to livestock-based manure fertilizers and fermented plant extracts application. PMID:24897025

The Influence of Ecological and Conventional Plant Production Systems on Soil Microbial Quality under Hops (Humulus lupulus

Directory of Open Access Journals (Sweden)

Karolina Oszust

2014-06-01

Full Text Available The knowledge about microorganisms—activity and diversity under hop production is still limited. We assumed that, different systems of hop production (within the same soil and climatic conditions significantly influence on the composition of soil microbial populations and its functional activity (metabolic potential. Therefore, we compared a set of soil microbial properties in the field experiment of two hop production systems (a ecological based on the use of probiotic preparations and organic fertilization (b conventional—with the use of chemical pesticides and mineral fertilizers. Soil analyses included following microbial properties: The total number microorganisms, a bunch of soil enzyme activities, the catabolic potential was also assessed following Biolog EcoPlates®. Moreover, the abundance of ammonia-oxidizing archaea (AOA was characterized by terminal restriction fragment length polymorphism analysis (T-RFLP of PCR ammonia monooxygenase α-subunit (amoA gene products. Conventional and ecological systems of hop production were able to affect soil microbial state in different seasonal manner. Favorable effect on soil microbial activity met under ecological, was more probably due to livestock-based manure and fermented plant extracts application. No negative influence on conventional hopyard soil was revealed. Both type of production fulfilled fertilizing demands. Under ecological production it was due to livestock-based manure fertilizers and fermented plant extracts application.

Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea

KAUST Repository

van de Water, Jeroen A. J. M.

2017-07-05

Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same \\'core microbiome\\' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of \\'core\\' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.

Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea.

Science.gov (United States)

van de Water, Jeroen A J M; Voolstra, Christian R; Rottier, Cecile; Cocito, Silvia; Peirano, Andrea; Allemand, Denis; Ferrier-Pagès, Christine

2018-01-01

Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same 'core microbiome' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of 'core' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.

Hydrogeological controls of variable microbial water quality in a complex subtropical karst system in Northern Vietnam

Science.gov (United States)

Ender, Anna; Goeppert, Nadine; Goldscheider, Nico

2018-05-01

Karst aquifers are particularly vulnerable to bacterial contamination. Especially in developing countries, poor microbial water quality poses a threat to human health. In order to develop effective groundwater protection strategies, a profound understanding of the hydrogeological setting is crucial. The goal of this study was to elucidate the relationships between high spatio-temporal variability in microbial contamination and the hydrogeological conditions. Based on extensive field studies, including mapping, tracer tests and hydrochemical analyses, a conceptual hydrogeological model was developed for a remote and geologically complex karst area in Northern Vietnam called Dong Van. Four different physicochemical water types were identified; the most important ones correspond to the karstified Bac Son and the fractured Na Quan aquifer. Alongside comprehensive investigation of the local hydrogeology, water quality was evaluated by analysis for three types of fecal indicator bacteria (FIB): Escherichia coli, enterococci and thermotolerant coliforms. The major findings are: (1) Springs from the Bac Son formation displayed the highest microbial contamination, while (2) springs that are involved in a polje series with connections to sinking streams were distinctly more contaminated than springs with a catchment area characterized by a more diffuse infiltration. (3) FIB concentrations are dependent on the season, with higher values under wet season conditions. Furthermore, (4) the type of spring capture also affects the water quality. Nevertheless, all studied springs were faecally impacted, along with several shallow wells within the confined karst aquifer. Based on these findings, effective protection strategies can be developed to improve groundwater quality.

Sediment nitrogen cycling rates and microbial abundance along a submerged vegetation gradient in a eutrophic lake.

Science.gov (United States)

Yao, Lu; Chen, Chengrong; Liu, Guihua; Liu, Wenzhi

2018-03-01

Decline of submerged vegetation is one of the most serious ecological problems in eutrophic lakes worldwide. Although restoration of submerged vegetation is widely assumed to enhance ecological functions (e.g., nitrogen removal) and aquatic biodiversity, the evidence for this assumption is very limited. Here, we investigated the spatio-temporal patterns of sediment potential nitrification, unamended denitrification and N 2 O production rates along a vegetation gradient in the Lake Honghu, where submerged vegetation was largely restored by prohibiting net-pen aquaculture. We also used five functional genes as markers to quantify the abundance of sediment nitrifying and denitrifying microorganisms. Results showed that unvegetated sediments supported greater nitrification rates than rhizosphere sediments of perennial or seasonal vegetation. However, the absence of submerged vegetation had no significant effect on denitrification and N 2 O production rates. Additionally, the abundance of functional microorganisms in sediments was not significantly different among vegetation types. Season had a strong effect on both nitrogen cycling processes and microbial abundances. The highest nitrification rates were observed in September, while the highest denitrification rates occurred in December. The temporal variation of sediment nitrification, denitrification and N 2 O production rates could be due to changes in water quality and sediment properties rather than submerged vegetation and microbial abundances. Our findings highlight that vegetation restoration in eutrophic lakes improves water quality but does not enhance sediment nitrogen removal rates and microbial abundances. Therefore, for reducing the N level in eutrophic lakes, major efforts should be made to control nutrients export from terrestrial ecosystems. Copyright © 2017 Elsevier B.V. All rights reserved.

Seasonality in the Austrian Economy: Common Seasonals and Forecasting

OpenAIRE

Kunst, Robert M.

1992-01-01

Abstract: Seasonal cointegration generalizes the idea of cointegration to processes with unit roots at frequencies different from 0. Here, also the dual notion of common trends, "common seasonals", is adopted for the seasonal case. Using a five-variable macroeconomic core system of the Austrian economy, it is demonstrated how common seasonals and seasonal cointegrating vectors look in practice. Statistical tests provide clear evidence on seasonal cointegration in the system. However, it is sh...

Effects of inorganic and organic amendment on soil chemical properties, enzyme activities, microbial community and soil quality in yellow clayey soil.

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Zhanjun Liu

Full Text Available Understanding the effects of external organic and inorganic components on soil fertility and quality is essential for improving low-yielding soils. We conducted a field study over two consecutive rice growing seasons to investigate the effect of applying chemical fertilizer (NPK, NPK plus green manure (NPKG, NPK plus pig manure (NPKM, and NPK plus straw (NPKS on the soil nutrient status, enzyme activities involved in C, N, P, and S cycling, microbial community and rice yields of yellow clayey soil. Results showed that the fertilized treatments significantly improved rice yields over the first three experimental seasons. Compared with the NPK treatment, organic amendments produced more favorable effects on soil productivity. Notably, the NPKM treatment exhibited the highest levels of nutrient availability, microbial biomass carbon (MBC, activities of most enzymes and the microbial community. This resulted in the highest soil quality index (SQI and rice yield, indicating better soil fertility and quality. Significant differences in enzyme activities and the microbial community were observed among the treatments, and redundancy analysis showed that MBC and available N were the key determinants affecting the soil enzyme activities and microbial community. The SQI score of the non-fertilized control (0.72 was comparable to that of the NPK (0.77, NPKG (0.81 and NPKS (0.79 treatments but significantly lower compared with NPKM (0.85. The significant correlation between rice yield and SQI suggests that SQI can be a useful to quantify soil quality changes caused by different agricultural management practices. The results indicate that application of NPK plus pig manure is the preferred option to enhance SOC accumulation, improve soil fertility and quality, and increase rice yield in yellow clayey soil.

Temperature sensitivity differences with depth and season between carbon, nitrogen, and phosphorus cycling enzyme activities in an ombrotrophic peatland system

Science.gov (United States)

Steinweg, J. M.; Kostka, J. E.; Hanson, P. J.; Schadt, C. W.

2017-12-01

Northern peatlands have large amounts of soil organic matter due to reduced decomposition. Breakdown of organic matter is initially mediated by extracellular enzymes, the activity of which may be controlled by temperature, moisture, and substrate availability, all of which vary seasonally throughout the year and with depth. In typical soils the majority of the microbial biomass and decomposition occurs within the top 30cm due to reduced organic matter inputs in the subsurface however peatlands by their very nature contain large amounts of organic matter throughout their depth profile. We hypothesized that potential enzyme activity would be greatest at the surface of the peat due to a larger microbial biomass compared to 40cm and 175cm below the surface and that temperature sensitivity would be greatest at the surface during winter but lowest during the summer due to high temperatures and enzyme efficiency. Peat samples were collected in February, July, and August 2012 from the DOE Spruce and Peatland Responses Under Climatic and Environmental Change project at Marcell Experimental Forest S1 bog. We measured potential activity of hydrolytic enzymes involved in three different nutrient cycles: beta-glucosidase (carbon), leucine amino peptidase (nitrogen), and phosphatase (phosphorus) at 15 temperature points ranging from 3°C to 65°C. Enzyme activity decreased with depth as expected but there was no concurrent change in activation energy (Ea). The reduction in enzyme activity with depth indicates a smaller pool which coincided with a decreased microbial biomass. Differences in enzyme activity with depth also mirrored the changes in peat composition from the acrotelm to the catotelm. Season did play a role in temperature sensitivity with Ea of β-glucosidase and phosphatase being the lowest in August as expected but leucine amino peptidase (a nitrogen acquiring enzyme) Ea was not influenced by season. As temperatures rise, especially in winter months, enzymatic

Microbial community biomass and structure in saline and non-saline soils associated with salt, boran tolerant poplar clones grown for the phytoremediation of selenium

Science.gov (United States)

The effect of naturally-occurring salts, boron (B), and selenium (Se) on soil microbial community composition associated with plants during different growing seasons used in bioremediation strategies is not known. This information is needed for developing sustainable remediation practices as soil mi...

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

NARCIS (Netherlands)

Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into

Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

KAUST Repository

Li, D.; Sharp, J. O.; Saikaly, Pascal; Ali, Shahjahan; Alidina, M.; Alarawi, M. S.; Keller, S.; Hoppe-Jones, C.; Drewes, J. E.

2012-01-01

This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

KAUST Repository

Li, D.

2012-07-13

This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

Dissolved organic carbon influences microbial community composition and diversity in managed aquifer recharge systems.

Science.gov (United States)

Li, Dong; Sharp, Jonathan O; Saikaly, Pascal E; Ali, Shahjahan; Alidina, Mazahirali; Alarawi, Mohammed S; Keller, Stephanie; Hoppe-Jones, Christiane; Drewes, Jörg E

2012-10-01

This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

Quantitative microbial risk assessment (QMRA) shows increased public health risk associated with exposure to river water under conditions of riverbed sediment resuspension.

Science.gov (United States)

Abia, Akebe Luther King; Ubomba-Jaswa, Eunice; Genthe, Bettina; Momba, Maggy Ndombo Benteke

2016-10-01

Although higher microbial concentrations have been reported in sediments than in the overlying water column, most quantitative microbial risk assessment (QMRA) studies have not clearly indicated the contribution of sediment-borne pathogens to estimated risks. Thus, the present study aimed at determining the public health risk associated with exposure to pathogenic bacteria in polluted river water under undisturbed conditions and conditions of sediment resuspension in the Apies River, Gauteng, South Africa. Microbial pathogens were isolated and identified using culture and molecular methods. The beta-Poisson dose-response model was used to estimate the probability of infection (Pi) with the various pathogens, following accidental/intentional ingestion of 1mL or 100mL (or 50mL) of untreated river water. Mean wet season Escherichia coli counts ranged between 5.8E+01 and 8.8E+04MPN/100mL (water column) and between 2.40E+03 and 1.28E+05MPN/100mL (sediments). Mean dry season E. coli counts ranged between 5.11E+00 and 3.40E+03MPN/100mL (water column) and between 5.09E+00 and 6.30E+03MPN/100mL (sediments). Overall (water and sediments) Vibrio cholerae was the most detected pathogen (58.8%) followed by Salmonella spp. (23.9%) and Shigella (10.1%). Ingestion of 1mL of river water could lead to 0%-4% and 1%-74% Pi with E. coli during the dry and wet season, respectively. During the dry season, the Pi with V. cholerae, Salmonella spp. and Shigella spp. were 0%-1.39%, 0%-4.11% and 0%-0.16% respectively, depending on volume of water ingested. The risks of infections with all microorganisms increased during the wet season. A 2-log increase in water E. coli count following sediments disturbance led to approximately 10 times higher Pi with E. coli than when sediments were undisturbed. Therefore, the use of the untreated water from the Apies River for drinking, household purposes or recreational activities poses a potential health risk to the users of the river. Copyright © 2016

Spatial and Temporal Microbial Patterns in a Tropical Macrotidal Estuary Subject to Urbanization

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Mirjam Kaestli

2017-07-01

Full Text Available Darwin Harbour in northern Australia is an estuary in the wet-dry tropics subject to increasing urbanization with localized water quality degradation due to increased nutrient loads from urban runoff and treated sewage effluent. Tropical estuaries are poorly studied compared to temperate systems and little is known about the microbial community-level response to nutrients. We aimed to examine the spatial and temporal patterns of the bacterial community and its association with abiotic factors. Since Darwin Harbour is macrotidal with strong seasonal patterns and mixing, we sought to determine if a human impact signal was discernible in the microbiota despite the strong hydrodynamic forces. Adopting a single impact–double reference design, we investigated the bacterial community using next-generation sequencing of the 16S rRNA gene from water and sediment from reference creeks and creeks affected by effluent and urban runoff. Samples were collected over two years during neap and spring tides, in the dry and wet seasons. Temporal drivers, namely seasons and tides had the strongest relationship to the water microbiota, reflecting the macrotidal nature of the estuary and its location in the wet-dry tropics. The neap-tide water microbiota provided the clearest spatial resolution while the sediment microbiota reflected current and past water conditions. Differences in patterns of the microbiota between different parts of the harbor reflected the harbor's complex hydrodynamics and bathymetry. Despite these variations, a microbial signature was discernible relating to specific effluent sources and urban runoff, and the composite of nutrient levels accounted for the major part of the explained variation in the microbiota followed by salinity. Our results confirm an overall good water quality but they also reflect the extent of some hypereutrophic areas. Our results show that the microbiota is a sensitive indicator to assess ecosystem health even in this

Virus Dynamics Are Influenced by Season, Tides and Advective Transport in Intertidal, Permeable Sediments.

Science.gov (United States)

Vandieken, Verona; Sabelhaus, Lara; Engelhardt, Tim

2017-01-01

Sandy surface sediments of tidal flats exhibit high microbial activity due to the fast and deep-reaching transport of oxygen and nutrients by porewater advection. On the other hand during low tide, limited transport results in nutrient and oxygen depletion concomitant to the accumulation of microbial metabolites. This study represents the first attempt to use flow-through reactors to investigate virus production, virus transport and the impact of tides and season in permeable sediments. The reactors were filled with intertidal sands of two sites (North beach site and backbarrier sand flat of Spiekeroog island in the German Wadden Sea) to best simulate advective porewater transport through the sediments. Virus and cell release along with oxygen consumption were measured in the effluents of reactors during continuous flow of water through the sediments as well as in tidal simulation experiments where alternating cycles with and without water flow (each for 6 h) were operated. The results showed net rates of virus production (0.3-13.2 × 10 6 viruses cm -3 h -1 ) and prokaryotic cell production (0.3-10.0 × 10 5 cells cm -3 h -1 ) as well as oxygen consumption rates (56-737 μmol l -1 h -1 ) to be linearly correlated reflecting differences in activity, season and location of the sediments. Calculations show that total virus turnover was fast with 2 to 4 days, whereas virus-mediated cell turnover was calculated to range between 5-13 or 33-91 days depending on the assumed burst sizes (number of viruses released upon cell lysis) of 14 or 100 viruses, respectively. During the experiments, the homogenized sediments in the reactors became vertically structured with decreasing microbial activities and increasing impact of viruses on prokaryotic mortality with depth. Tidal simulation clearly showed a strong accumulation of viruses and cells in the top sections of the reactors when the flow was halted indicating a consistently high virus production during low tide. In

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.

Directory of Open Access Journals (Sweden)

Douglas B Rusch

2007-03-01

Full Text Available The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp. Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1 extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2 numerous changes in gene content some with direct adaptive implications; and (3 hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic

Microbial Rechargeable Battery

NARCIS (Netherlands)

Molenaar, Sam D.; Mol, Annemerel R.; Sleutels, Tom H.J.A.; Heijne, Ter Annemiek; Buisman, Cees J.N.

2016-01-01

Bioelectrochemical systems hold potential for both conversion of electricity into chemicals through microbial electrosynthesis (MES) and the provision of electrical power by oxidation of organics using microbial fuel cells (MFCs). This study provides a proof of concept for a microbial

Contamination of Fresh Produce by Microbial Indicators on Farms and in Packing Facilities: Elucidation of Environmental Routes.

Science.gov (United States)

Bartz, Faith E; Lickness, Jacquelyn Sunshine; Heredia, Norma; Fabiszewski de Aceituno, Anna; Newman, Kira L; Hodge, Domonique Watson; Jaykus, Lee-Ann; García, Santos; Leon, Juan S

2017-06-01

To improve food safety on farms, it is critical to quantify the impact of environmental microbial contamination sources on fresh produce. However, studies are hampered by difficulties achieving study designs with powered sample sizes to elucidate relationships between environmental and produce contamination. Our goal was to quantify, in the agricultural production environment, the relationship between microbial contamination on hands, soil, and water and contamination on fresh produce. In 11 farms and packing facilities in northern Mexico, we applied a matched study design: composite samples ( n = 636, equivalent to 11,046 units) of produce rinses were matched to water, soil, and worker hand rinses during two growing seasons. Microbial indicators (coliforms, Escherichia coli , Enterococcus spp., and somatic coliphage) were quantified from composite samples. Statistical measures of association and correlations were calculated through Spearman's correlation, linear regression, and logistic regression models. The concentrations of all microbial indicators were positively correlated between produce and hands (ρ range, 0.41 to 0.75; P contamination of soil and water and contamination of produce. This methodology provides a foundation for future field studies, and results highlight the need for interventions surrounding farmworker hygiene and sanitation to reduce microbial contamination of farmworkers' hands. IMPORTANCE This study of the relationships between microbes on produce and in the farm environment can be used to support the design of targeted interventions to prevent or reduce microbial contamination of fresh produce with associated reductions in foodborne illness. Copyright © 2017 American Society for Microbiology.

Microbial Removal Efficiency of UV in Tehran Shahid Mahallati Wastewater Treatment Plant

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Reza Dabbagh

2009-03-01

Full Text Available Shahid Mahallati Wastewater Treatment Plant was selected for installing a UV disinfection unit to investigate its germicidal effect on microbial removal. Low pressure mercury lamps were used to generate germicidal ultraviolet radiation (UV-C. The UV system was operated over a period of 6 months that included both warm and cold seasons. A maximum UV disinfection efficiency of 14.4m3/h was recorded for the system on the basis of design criteria within turbidity ranges of 9 to 32 NTU. The minimum UV dose applied in the UV unit was 40000 µW.s/cm2 and the highest bacterial density in the UV unit influent was 5.6*107. Effluent total coliform or fecal coliform enumeration after exposure to UV ray showed the microbial density decreasing from four logs, or 99.99%, to as high as six logs, or 99.9999% removal efficiency, under different conditions. Effluent microbial densities in terms of total and fecal coliforms were below 1000MPN/100mL and 400MPN/100mL, respectively. These values comply with wastewater discharge or agricultural irrigation standards according to Iran Department of Environment. From our results, it is concluded that UV disinfection may be an effective technique for wastewater disinfection in Iranian wastewater treatment plants.

International Clostridium difficile animal strain collection and large diversity of animal associated strains

DEFF Research Database (Denmark)

Janezic, Sandra; Zidaric, Valerija; Pardon, Bart

2014-01-01

Background: Clostridium difficile is an important cause of intestinal infections in some animal species and animals might be a reservoir for community associated human infections. Here we describe a collection of animal associated C. difficile strains from 12 countries based on inclusion criteria...... of one strain (PCR ribotype) per animal species per laboratory. Results: Altogether 112 isolates were collected and distributed into 38 PCR ribotypes with agarose based approach and 50 PCR ribotypes with sequencer based approach. Four PCR ribotypes were most prevalent in terms of number of isolates...... as well as in terms of number of different host species: 078 (14.3% of isolates; 4 hosts), 014/020 (11.6%; 8 hosts); 002 (5.4%; 4 hosts) and 012 (5.4%; 5 hosts). Two animal hosts were best represented; cattle with 31 isolates (20 PCR ribotypes; 7 countries) and pigs with 31 isolates (16 PCR ribotypes; 10...

Enhanced surveillance of Clostridium difficile infection occurring outside hospital, England, 2011 to 2013.

Science.gov (United States)

Fawley, Warren N; Davies, Kerrie A; Morris, Trefor; Parnell, Peter; Howe, Robin; Wilcox, Mark H

2016-07-21

There are limited national epidemiological data for community-associated (CA)-Clostridium difficile infections (CDIs). Between March 2011 and March 2013, laboratories in England submitted to the Clostridium difficile Ribotyping Network (CDRN) up to 10 diarrhoeal faecal samples from successive patients with CA-CDI, defined here as C. difficile toxin-positive diarrhoea commencing outside hospital (or less than 48 hours after hospital admission), including those cases associated with community-based residential care, with no discharge from hospital within the previous 12 weeks. Patient demographics and C. difficile PCR ribotypes were compared for CA-CDIs in our study and presumed healthcare-associated (HA) CDIs via CDRN. Ribotype diversity indices, ranking and relative prevalences were very similar in CA- vs HA-CDIs, although ribotypes 002 (p ≤ 0.0001),020 (p = 0.009) and 056 (p < 0.0001) predominated in CA-CDIs; ribotype 027 (p = 0.01) predominated in HA-CDIs. Epidemic ribotypes 027 and 078 predominated in institutional residents with CDI (including care/nursing homes) compared with people with CDI living at home. Ribotype diversity decreased with increasing age in HA-CDIs, but not in CA-CDIs. Ribotype 078 CA-CDIs were significantly more common in elderly people (3.4% (6/174) vs 8.7% (45/519) in those aged < 65 and ≥ 65 years, respectively; p = 0.019). No antibiotics were prescribed in the previous four weeks in about twofold more CA-CDI vs HAs (38.6% (129/334) vs 20.3% (1,226/6,028); p < 0.0001). We found very similar ribotype distributions in CA- and HA-CDIs, although a few ribotypes significantly predominated in one setting. These national data emphasise the close interplay between, and likely common reservoirs for, CDIs, particularly when epidemic strains are not dominant. This article is copyright of The Authors, 2016.

Soil Microbial Community Contribution to Small Headwater Stream Metabolism.

Science.gov (United States)

Clapcott, J. E.; Gooderham, J. P.; Barmuta, L. A.; Davies, P. E.

2005-05-01

The temporal dynamics of sediment respiration were examined in seven small headwater streams in forested catchments in 2004. A strong seasonal response was observed with higher respiration rates in depositional zones than in gravel runs. The data were also examined in the context of proportional habitat distributions that highlighted the importance of high flow events in shaping whole stream metabolic budgets. This study specifically examines the question of terrestrial soil respiration contribution to whole stream metabolism by the controlled inundation of terrestrial soils. The experiment included six experimentally inundated terrestrial zones, six terrestrial controls, and six in-stream depositional zones. Sediment bacterial respiration was measured using 14C leucine incorporation and cotton strip bioassays were also employed to provide an indicative measure of sediment microbial activity. Despite high variability and exhibiting significantly lower bacterial activity than in-stream sediments, modelling using flow data and habitat mapping illustrated the important contribution of terrestrial soil respiration to the whole stream metabolic budgets of small headwater streams. In addition, microbial community composition examined using phospholipid fatty acid analysis clearly differentiated between terrestrial and aquatic communities. Freshly inundated terrestrial communities remained similar to un-inundated controls after 28 days.

Microbial biosensors

International Nuclear Information System (INIS)

Le Yu; Chen, Wilfred; Mulchandani, Ashok

2006-01-01

A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

Childhood microbial keratitis

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Abdullah G Al Otaibi

2012-01-01

Conclusion: Children with suspected microbial keratitis require comprehensive evaluation and management. Early recognition, identifying the predisposing factors and etiological microbial organisms, and instituting appropriate treatment measures have a crucial role in outcome. Ocular trauma was the leading cause of childhood microbial keratitis in our study.

Methanotrophic community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia

Directory of Open Access Journals (Sweden)

Mónica Torres-Beltrán

2016-12-01

Full Text Available Marine oxygen minimum zones (OMZs play disproportionate roles in nutrient and climate active trace gas cycling including nitrous oxide and methane, in the ocean. OMZs are currently expanding due to climate change making it increasingly important to identify microbial controls on trace gas cycling at the individual, population and community levels. Here we present a two-year survey of the microbial community along seasonal redox gradients in Saanich Inlet focused on identifying microbial agents driving methane oxidation. Although methanotrophs were rare, we identified three uncultivated groups affiliated with particulate methane monooxygenase (pMMO encoding phylogenetic groups (OPU, and methanotrophic symbionts as primary drivers of methane oxidation in Saanich Inlet. Distribution and activity patterns for these three groups were consistent with niche partitioning that became increasingly resolved during water column stratification. Moreover co-occurrence analysis combined with multi-level indicator species analysis revealed significant correlations between operational taxonomic units affiliated with Methylophaga, Methylophilales, SAR324, Verrucomicrobia, and Planctomycetes with OPUs and methanotrophic symbiont groups. Taken together these observations shed new light on the composition, dynamics, and potential interspecific interactions of microbes associated with CH4 cycling in the Saanich Inlet water column, provide a baseline for comparison between coastal and open ocean OMZs and support the potential role of OPUs, and methanotrophic symbiont groups as a widely distributed pelagic sink for CH4 along continental margins.

Faecal shedding of antimicrobial-resistant Clostridium difficile strains by dogs.

Science.gov (United States)

Álvarez-Pérez, S; Blanco, J L; Peláez, T; Lanzarot, M P; Harmanus, C; Kuijper, E; García, M E

2015-03-01

To longitudinally assess the shedding of antimicrobial resistant Clostridium difficile strains by clinically healthy dogs raised at breeding facilities. 18 puppies from three different litters (#1, 2 and 3) were sampled weekly from parturition to day 20-55 postpartum. Faecal samples from the mothers of litters #2 and 3 were also available for analysis. Bacterial isolates were ribotyped, tested for in vitro antimicrobial susceptibility and further characterised. C. difficile was recovered from all sampled animals of litters #1 and 2, and a third of puppies from litter #3, but marked differences in C. difficile recovery were detected in different age groups (0-100%). Recovered PCR ribotypes included 056 (22 isolates), 010 (6 isolates), 078 and 213 (2 isolates each), and 009 and 020 (1 isolate each). Different ribotypes were shed by four individual animals. Regardless of their origin and ribotype, all isolates demonstrated full resistance to levofloxacin. Additionally, all but one isolate (belonging to ribotype 078) were resistant to ertapenem, and all ribotype 010 isolates displayed high-level resistance to clindamycin, clarithromycin and erythromycin. A single ribotype 078 isolate showed metronidazole heteroresistance. Healthy dogs can shed antimicrobial-resistant C. difficile strains. © 2014 British Small Animal Veterinary Association.

Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea

OpenAIRE

Stief, Peter; Fuchs-Ocklenburg, Silvia; Kamp, Anja; Manohar, Cathrine-Sumathi; Houbraken, Jos; Boekhout, Teun; de Beer, Dirk; Stoeck, Thorsten

2014-01-01

Background A wealth of microbial eukaryotes is adapted to life in oxygen-deficient marine environments. Evidence is accumulating that some of these eukaryotes survive anoxia by employing dissimilatory nitrate reduction, a strategy that otherwise is widespread in prokaryotes. Here, we report on the anaerobic nitrate metabolism of the fungus Aspergillus terreus (isolate An-4) that was obtained from sediment in the seasonal oxygen minimum zone in the Arabian Sea, a globally important site of oce...

Groundwater mixing at fracture intersections triggers massive iron-rich microbial mats

Science.gov (United States)

Bochet, O.; Le Borgne, T.; Bethencourt, L.; Aquilina, L.; Dufresne, A.; Pédrot, M.; Farasin, J.; Abbott, B. W.; Labasque, T.; Chatton, E.; Lavenant, N.; Petton, C.

2017-12-01

While most freshwater on Earth resides and flows in groundwater systems, these deep subsurface environments are often assumed to have little biogeochemical activity compared to surface environments. Here we report a massive microbial mat of iron-oxidizing bacteria, flourishing 60 meters below the surface, far below the mixing zone where most microbial activity is believed to occur. The abundance of microtubular structures in the mat hinted at the prevalence of of Leptothrix ochracea, but metagenomic analysis revealed a diverse consortium of iron-oxidizing bacteria dominated by unknown members of the Gallionellaceae family. This deep biogeochemical hot spot formed at the intersection of bedrock fractures, which maintain redox gradients by mixing water with different residence times and chemical compositions. Using measured fracture properties and hydrological conditions we developed a quantitative model to simulate the reactive zone where such deep hot spots could occur. While seasonal fluctuations are generally thought to decrease with depth, we found that meter-scale changes in water table level moved the depth of the reactive zone hundreds of meters because the microaerophilic threshold for ironoxidizers is highly sensitive to changes in mixing rates at fracture intersections. These results demonstrate that dynamic microbial communities can be sustained deep below the surface in bedrock fractures. Given the ubiquity of fractures at multiple scales in Earth's subsurface, such deep hot spots may strongly influence global biogeochemical cycles.

Development of a typing system for epidemiological studies of porcine toxin-producing Pasteurella multocida ssp. multocida in Denmark

DEFF Research Database (Denmark)

Fussing, V.; Nielsen, Jens; Bisgaard, M.

1999-01-01

The aim of the present study was to evaluate capsular-typing, plasmid-profiling, phage-typing and ribotyping for epidemiological studies of toxin-producing Pasteurella multocida ssp. multocida in Denmark. The evaluation of methods was based on 68 strains from nasal swabs and 14 strains from...... by HindIII ribotyping, as 85% of isolates from all herds were assigned to one ribotype. In conclusion, HindIII ribotyping seems to represent a useful tool for epidemiological studies of toxigenic P. multocida ssp. multocida....

Altitudinal, seasonal and interannual shifts in microbial communities and chemical composition of soil organic matter in Alpine forest soils

Czech Academy of Sciences Publication Activity Database

Siles, J.A.; Cajthaml, Tomáš; Filipová, Alena; Minerbi, S.; Margesin, R.

2017-01-01

Roč. 112, SEP 2017 (2017), s. 1-13 ISSN 0038-0717 Institutional support: RVO:61388971 Keywords : Elevational (altitudinal) gradient * Forest * Microbial communit Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 4.857, year: 2016

Microbial community dynamics in the forefield of glaciers.

Science.gov (United States)

Bradley, James A; Singarayer, Joy S; Anesio, Alexandre M

2014-11-22

Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.

Seasonal patterns in soil N availability in the arctic tundra in response to accelerated snowmelt and warming

Science.gov (United States)

Darrouzet-Nardi, A.; Wallenstein, M. D.; Steltzer, H.; Sullivan, P.; Melle, C.; Segal, A.; Weintraub, M. N.

2010-12-01

Arctic soils contain large stocks of carbon (C) and may act as a significant CO2 source in response to climate warming. However, nitrogen (N) availability limits both plant growth and decomposition in many Arctic sites, and may thus be a key constraint on climate-carbon feedbacks. While current models of tundra ecosystems and their responses to climate change assume that N limits plant growth and C limits decomposition, there is strong evidence to the contrary showing that N can also limit decomposition. For example, the production of both new microbial biomass and enzymes that degrade organic matter appear to be limited by N during the summer. N availability is strongly seasonal: we have previously observed relatively high availability early in the growing season followed by a pronounced crash in tussock tundra soils. To investigate the drivers of N availability throughout the season, we used a field manipulation of tussock tundra growing season length (~4 days acceleration of snowmelt) and air temperature (open top chambers) and a laboratory soil N addition in both early and late season. Nutrient availability throughout the field season was measured at high temporal resolution (25 measurements from soil thaw through early plant senescence). Results from a laboratory experiment in which N was added to early season and late season soils suggests that soil respiration is in fact N limited at both times of the season, though this limitation is temperature dependent with effects most pronounced at 10°C. High-resolution measurements of nutrients in the soil solution and extractable N throughout the season showed that although a nutrient crash in N can be observed mid-season, N availability can still fluctuate later in the season. Finally, effects of the extended growing season and increased air temperature have so far had few effects on soil nutrient N dynamics throughout the summer growing season, suggesting either an insensitivity of N availability to these

Detection of Clostridium difficile infection clusters, using the temporal scan statistic, in a community hospital in southern Ontario, Canada, 2006-2011.

Science.gov (United States)

Faires, Meredith C; Pearl, David L; Ciccotelli, William A; Berke, Olaf; Reid-Smith, Richard J; Weese, J Scott

2014-05-12

In hospitals, Clostridium difficile infection (CDI) surveillance relies on unvalidated guidelines or threshold criteria to identify outbreaks. This can result in false-positive and -negative cluster alarms. The application of statistical methods to identify and understand CDI clusters may be a useful alternative or complement to standard surveillance techniques. The objectives of this study were to investigate the utility of the temporal scan statistic for detecting CDI clusters and determine if there are significant differences in the rate of CDI cases by month, season, and year in a community hospital. Bacteriology reports of patients identified with a CDI from August 2006 to February 2011 were collected. For patients detected with CDI from March 2010 to February 2011, stool specimens were obtained. Clostridium difficile isolates were characterized by ribotyping and investigated for the presence of toxin genes by PCR. CDI clusters were investigated using a retrospective temporal scan test statistic. Statistically significant clusters were compared to known CDI outbreaks within the hospital. A negative binomial regression model was used to identify associations between year, season, month and the rate of CDI cases. Overall, 86 CDI cases were identified. Eighteen specimens were analyzed and nine ribotypes were classified with ribotype 027 (n = 6) the most prevalent. The temporal scan statistic identified significant CDI clusters at the hospital (n = 5), service (n = 6), and ward (n = 4) levels (P ≤ 0.05). Three clusters were concordant with the one C. difficile outbreak identified by hospital personnel. Two clusters were identified as potential outbreaks. The negative binomial model indicated years 2007-2010 (P ≤ 0.05) had decreased CDI rates compared to 2006 and spring had an increased CDI rate compared to the fall (P = 0.023). Application of the temporal scan statistic identified several clusters, including potential outbreaks not detected by hospital

Diversity of microbial plankton across the Three Gorges Dam of the Yangtze River, China

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Shang Wang

2012-05-01

Full Text Available The Three Gorges Dam (TGD of the Yangtze River, China, is one of the largest irrigation and hydroelectric engineering projects in the world. The effects of huge man-made projects like TGD on fauna and macrophyte are obvious, mainly through changes of water dynamics and flow pattern; however, it is less clear how microorganisms respond to such changes. This research was aimed to examine differences in microbial diversity at different seasons and locations (in front of and behind the TGD. In addition, differences between particle-attached and free-living communities were also examined. The community structures of total and potentially active microorganisms in the water columns behind and in front of the TGD were analyzed with the DNA- and RNA-based 16S rRNA gene phylogenetic approaches over three different seasons. Clone libraries of 16S rRNA genes were prepared after amplification from extracted DNA and, for some samples, after preparing cDNA from extracted rRNA. Differences were observed between sites at different seasons and between free-living and particle-attached communities. Both bacterial and archaeal communities were more diverse in summer than in winter, due to higher nutrient levels and warmer temperature in summer than in winter. Particle-attached microorganisms were more diverse than free-living communities, possibly because of higher nutrient levels and heterogeneous geochemical micro-environments in particles. Spatial variations in bacterial community structure were observed, i.e., the water reservoir behind the TGD (upstream hosted more diverse bacterial populations than in front of the dam (downstream, because of diverse sources of sediments and waters from upstream to the reservoir. These results have important implications for our understanding of responses of microbial communities to environmental changes in river ecosystems affected by dam construction.

Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata.

Science.gov (United States)

Sharp, Koty H; Pratte, Zoe A; Kerwin, Allison H; Rotjan, Randi D; Stewart, Frank J

2017-09-15

Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome community composition. Change in season had a strong effect on A. poculata microbiome composition. The seasonal shift was greatest upon the winter to spring transition, during which time A. poculata microbiome composition became more similar among host individuals. Within each of the four seasons, microbiome composition differed significantly from that of surrounding seawater but was surprisingly uniform between symbiotic and aposymbiotic corals, even in summer, when differences in Symbiodinium density between brown and white colonies are the highest, indicating that the observed seasonal shifts are not likely due to fluctuations in Symbiodinium density. Our results suggest that symbiotic state may not be a primary driver of coral microbial community organization in A. poculata, which is a surprise given the long-held assumption that excess photosynthate is of importance to coral-associated microbes. Rather, other environmental or host factors, in this case, seasonal changes in host physiology associated with winter quiescence, may drive microbiome diversity. Additional studies of A. poculata and other facultatively symbiotic corals will provide important comparisons to studies of reef-building tropical corals and therefore

Decreasing but still significant facilitation effect of cold-season macrophytes on wetlands purification function during cold winter.

Science.gov (United States)

Zou, Xiangxu; Zhang, Hui; Zuo, Jie; Wang, Penghe; Zhao, Dehua; An, Shuqing

2016-06-01

To identify the facilitation effect of a cool-season aquatic macrophyte (FEam) for use in effluent purification via constructed floating wetlands (CFWs) and to determine the possible pathways used during a winter period with an average temperature of less than 5 °C, pilot-scale CFWs were planted with the cold-season macrophyte Oenanthe clecumbens and were operated as batch systems. Although some leaves withered, the roots retained relatively high levels of activity during the winter, which had average air and water temperatures of 3.63 and 5.04 °C, respectively. The N and P removal efficiencies in CFWs decreased significantly in winter relative to those in late autumn. The presence of cool-season plants resulted in significant improvements in N and P removal, with a FEam of 15.23-25.86% in winter. Microbial N removal accounted for 71.57% of the total N removed in winter, and the decrease in plant uptake was the dominant factor in the wintertime decrease in N removal relative to that in late autumn. These results demonstrate the importance of cold-season plants in CFWs for the treatment of secondary effluent during cold winters.

Rapid spectrofluorometric screening of poly-hydroxyalkanoate-producing bacteria from microbial mats.

Science.gov (United States)

Berlanga, Mercedes; Montero, M T; Fernández-Borrell, Jordi; Guerrero, Ricardo

2006-06-01

Microbial mat ecosystems are characterized by both seasonal and diel fluctuations in several physicochemical variables, so that resident microorganisms must frequently adapt to the changing conditions of their environment. It has been pointed out that, under stress conditions, bacterial cells with higher contents of poly-hydroxyalkanoates (PHA) survive longer than those with lower PHA content. In the present study, PHA-producing strains from Ebro Delta microbial mats were selected using the Nile red dying technique and the relative accumulation of PHA was monitored during further laboratory cultivation. The number of heterotrophic isolates in trypticase soy agar (TSA) was ca. 107 colony-forming units/g microbial mat. Of these, 100 randomly chosen colonies were replicated on mineral salt agar limited in nitrogen, and Nile red was added to the medium to detect PHA. Orange fluorescence, produced upon binding of the dye to polymer granules in the cell, was detected in approximately 10% of the replicated heterotrophic isolates. The kinetics of PHA accumulation in Pseudomonas putida, and P. oleovorans were compared with those of several of the environmental isolates spectrofluorometry. PHA accumulation, measured as relative fluorescence intensity, resulted in a steady-state concentration after 48 h of incubation in all strains assayed. At 72 h, the maximum fluorescence intensity of each strain incubated with glucose and fructose was usually similar. MAT-28 strain accumulated more PHA than the other isolates. The results show that data obtained from environmental isolates can highly improve studies based on modeling-simulation programs, and that microbial mats constitute an excellent source for the isolation of PHA-producing strains with industrial applications.

Reducing microbial contamination on wastewater-irrigated lettuce by cessation of irrigation before harvesting

DEFF Research Database (Denmark)

Keraita, Bernard; Konradsen, Flemming; Drechsel, Pay

2007-01-01

OBJECTIVE: To assess the effectiveness of cessation of irrigation before harvesting in reducing microbial contamination of lettuce irrigated with wastewater in urban vegetable farming in Ghana. METHODS: Assessment was done under actual field conditions with urban vegetable farmers in Ghana. Trials...... were arranged in completely randomized block design and done both in the dry and wet seasons. Seven hundred and twenty-six lettuce samples and 36 water samples were analysed for thermotolerant coliforms and helminth eggs. RESULTS: On average, 0.65 log units for indicator thermotolerant coliforms and 0.......4 helminth eggs per 100 g of lettuce were removed on each non-irrigated day from lettuce in the dry season. This corresponded to a daily loss of 1.4 tonnes/ha of fresh weight of lettuce. As an input for exposure analysis to make risk estimates, the decay coefficient, k, for thermotolerant coliforms was 0...

A Broader View: Microbial Enzymes and Their Relevance in Industries, Medicine, and Beyond

Science.gov (United States)

Bose, Sutapa; Rai, Vivek

2013-01-01

Enzymes are the large biomolecules that are required for the numerous chemical interconversions that sustain life. They accelerate all the metabolic processes in the body and carry out a specific task. Enzymes are highly efficient, which can increase reaction rates by 100 million to 10 billion times faster than any normal chemical reaction. Due to development in recombinant technology and protein engineering, enzymes have evolved as an important molecule that has been widely used in different industrial and therapeutical purposes. Microbial enzymes are currently acquiring much attention with rapid development of enzyme technology. Microbial enzymes are preferred due to their economic feasibility, high yields, consistency, ease of product modification and optimization, regular supply due to absence of seasonal fluctuations, rapid growth of microbes on inexpensive media, stability, and greater catalytic activity. Microbial enzymes play a major role in the diagnosis, treatment, biochemical investigation, and monitoring of various dreaded diseases. Amylase and lipase are two very important enzymes that have been vastly studied and have great importance in different industries and therapeutic industry. In this review, an approach has been made to highlight the importance of different enzymes with special emphasis on amylase and lipase in the different industrial and medical fields. PMID:24106701

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

OpenAIRE

Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) w...

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

OpenAIRE

Timmers, Ruud A.; Rothballer, Michael; Strik, David P. B. T. B.; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode–rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) w...

Long-term reactive nitrogen loading alters soil carbon and microbial community properties in a subalpine forest ecosystem

Science.gov (United States)

Boot, Claudia M.; Hall, Ed K.; Denef, Karolien; Baron, Jill S.

2016-01-01

Elevated nitrogen (N) deposition due to increased fossil fuel combustion and agricultural practices has altered global carbon (C) cycling. Additions of reactive N to N-limited environments are typically accompanied by increases in plant biomass. Soil C dynamics, however, have shown a range of different responses to the addition of reactive N that seem to be ecosystem dependent. We evaluated the effect of N amendments on biogeochemical characteristics and microbial responses of subalpine forest organic soils in order to develop a mechanistic understanding of how soils are affected by N amendments in subalpine ecosystems. We measured a suite of responses across three years (2011–2013) during two seasons (spring and fall). Following 17 years of N amendments, fertilized soils were more acidic (control mean 5.09, fertilized mean 4.68), and had lower %C (control mean 33.7% C, fertilized mean 29.8% C) and microbial biomass C by 22% relative to control plots. Shifts in biogeochemical properties in fertilized plots were associated with an altered microbial community driven by reduced arbuscular mycorrhizal (control mean 3.2 mol%, fertilized mean 2.5 mol%) and saprotrophic fungal groups (control mean 17.0 mol%, fertilized mean 15.2 mol%), as well as a decrease in N degrading microbial enzyme activity. Our results suggest that decreases in soil C in subalpine forests were in part driven by increased microbial degradation of soil organic matter and reduced inputs to soil organic matter in the form of microbial biomass.

Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model.

Science.gov (United States)

Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

2015-03-01

A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs.

Short-term Effect of Nitrogen Addition on Microbial and Root Respiration in an Alpine Spruce Ecosystem

Directory of Open Access Journals (Sweden)

Jian Wang1

2017-03-01

Full Text Available Soil respiration plays an important role in the carbon (C flux of the global C cycle and is greatly affected by nitrogen (N additions in the form of deposition or fertilization. The aim of this study was to investigate the response of total soil respiration (Rs, microbial respiration (Rm, and root respiration (Rr to short-term N addition and the potential mechanisms of short-term N deposition influencing soil respiration in an alpine spruce ecosystem. Four N treatment levels (0, 50, 100, 150 kg N ha-1 year-1 were applied monthly in a Picea balfouriana (commonly known as "alpine spruce" plantation beginning in November 2013 and Rs, Rm, and Rr were measured from May to November 2014. The results show that simulated N depositions stimulate Rs, Rm, and Rr and the beneficial effects decreased along N gradients from hourly to seasonal scales. The seasonal temperature coefficients (Q10 of Rs, Rm, and Rr ranged from 2.50 to 3.8, 2.99 to 4.63, and 1.86 to 2.96, while the diurnal Q10 ranged from 1.71 to 2.04, 1.89 to 2.32, 1.42 to 1.75, and there was a similar trend with soil respiration along N gradients. In addition, Rr showed significant positive correlation with fine root biomass, and Rm was likely driven by soil enzyme related to the microbial C cycle in the growing season. Our results indicate that short-term N addition stimulated fine root biomass and soil enzymatic activity to bring about a potential increase in soil respiration rates under low-N addition, while the opposite occurred under high-N addition.

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

Directory of Open Access Journals (Sweden)

Nam-Il Won

2017-01-01

Full Text Available The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA. However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene, we analyzed and compared seawater and sediment communities between sand mining and control (natural sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA.

Proceedings of the 8. International Symposium on Microbial Ecology : microbial biosystems : new frontiers

International Nuclear Information System (INIS)

Bell, C.R.; Brylinsky, M.; Johnson-Green, P.

2000-01-01

A wide range of disciplines were presented at this conference which reflected the importance of microbial ecology and provided an understanding of the factors that determine the growth and activities of microorganisms. The conference attracted 1444 delegates from 54 countries. The research emerging from the rapidly expanding frontier of microbial ecosystems was presented in 62 oral presentation and 817 poster presentations. The two volumes of these proceedings presented a total of 27 areas in microbial ecology, some of which included terrestrial biosystems, aquatic, estuarine, surface and subsurface microbial ecology. Other topics included bioremediation, microbial ecology in industry and microbial ecology of oil fields. Some of the papers highlighted the research that is underway to determine the feasibility of using microorganisms for enhanced oil recovery (EOR). Research has shown that microbial EOR can increase production at lower costs than conventional oil recovery. The use of bacteria has also proven to be a feasible treatment method in the biodegradation of hydrocarbons associated with oil spills. refs., tabs., figs

Influence of microbial community diversity and function on pollutant removal in ecological wastewater treatment.

Science.gov (United States)

Bai, Yaohui; Huo, Yang; Liao, Kailingli; Qu, Jiuhui

2017-10-01

Traditional wastewater treatments based on activated sludge often encounter the problems of bulking and foaming, as well as malodor. To solve these problems, new treatment technologies have emerged in recent decades, including the ecological wastewater treatment process, which introduces selected local plants into the treatment system. With a focus on the underlying mechanisms of the ecological treatment process, we explored the microbial community biomass, composition, and function in the treatment system to understand the microbial growth in this system and its role in pollutant removal. Flow cytometry analysis revealed that ecological treatment significantly decreased influent bacterial quantity, with around 80% removal. 16S rRNA gene sequencing showed that the ecological treatment also altered the bacterial community structure of the wastewater, leading to a significant change in Comamonadaceae in the effluent. In the internal ecological system, because most of microbes aggregate in the plant rhizosphere and the sludge under plant roots, we selected two plant species (Nerium oleander and Arundo donax) to study the characteristics of rhizosphere and sludge microbes. Metagenomic results showed that the microbial community composition and function differed between the two species, and the microbial communities of A. donax were more sensitive to seasonal effects. Combined with their greater biomass and abundance of metabolic genes, microbes associated with N. oleander showed a greater contribution to pollutant removal. Further, the biodegradation pathways of some micropollutants, e.g., atrazine, were estimated.

[Characterization and microbial community shifts of rice strawdegrading microbial consortia].

Science.gov (United States)

Wang, Chunfang; Ma, Shichun; Huang, Yan; Liu, Laiyan; Fan, Hui; Deng, Yu

2016-12-04

To study the relationship between microbial community and degradation rate of rice straw, we compared and analyzed cellulose-decomposing ability, microbial community structures and shifts of microbial consortia F1 and F2. We determined exoglucanase activity by 3, 5-dinitrosalicylic acid colorimetry. We determined content of cellulose, hemicellulose and lignin in rice straw by Van Soest method, and calculated degradation rates of rice straw by the weight changes before and after a 10-day incubation. We analyzed and compared the microbial communities and functional microbiology shifts by clone libraries, Miseq analysis and real time-PCR based on the 16S rRNA gene and cel48 genes. Total degradation rate, cellulose, and hemicellulose degradation rate of microbial consortia F1 were significantly higher than that of F2. The variation trend of exoglucanase activity in both microbial consortia F1 and F2 was consistent with that of cel48 gene copies. Microbial diversity of F1 was complex with aerobic bacteria as dominant species, whereas that of F2 was simple with a high proportion of anaerobic cellulose decomposing bacteria in the later stage of incubation. In the first 4 days, unclassified Bacillales and Bacillus were dominant in both F1 and F2. The dominant species and abundance became different after 4-day incubation, Bacteroidetes and Firmicutes were dominant phyla of F1 and F2, respectively. Although Petrimonas and Pusillimonas were common dominant species in F1 and F2, abundance of Petrimonas in F2 (38.30%) was significantly higher than that in F1 (9.47%), and the abundance of Clostridiales OPB54 in F2 increased to 14.85% after 8-day incubation. The abundance of cel48 gene related with cellulose degradation rate and exoglucanase activity, and cel48 gene has the potential as a molecular marker to monitor the process of cellulose degradation. Microbial community structure has a remarkable impact on the degradation efficiency of straw cellulose, and Petrimonas

Amount, composition and seasonality of dissolved organic carbon and nitrogen export from agriculture in contrasting climates

DEFF Research Database (Denmark)

Graeber, Daniel; Meerhof, Mariana; Zwirnmann, Elke

2014-01-01

Agricultural catchments are potentially important but often neglected sources of dissolved organic matter (DOM), of which a large part is dissolved organic carbon (DOC) and nitrogen (DON). DOC is an important source of aquatic microbial respiration and DON may be an important source of nitrogen...... to aquatic ecosystems. However, there is still a lack of comprehensive studies on the amount, composition and seasonality of DOM export from agricultural catchments in different climates. The aim of our study was to assess the amount, composition and seasonality of DOM in a total of four streams in the wet......-temperate and subtropical climate of Denmark and Uruguay, respectively. In each climate, we investigated one stream with extensive agriculture (mostly pasture) and one stream with intensive agriculture (mostly intensively used arable land) in the catchment. We sampled each stream taking grab samples fortnightly for two...

Microbial conversion technologies

Energy Technology Data Exchange (ETDEWEB)

Lau, P. [National Research Council of Canada, Ottawa, ON (Canada). Bioconversion and Sustainable Development

2006-07-01

Microbes are a biomass and an valuable resource. This presentation discussed microbial conversion technologies along with background information on microbial cells, their characteristics and microbial diversity. Untapped opportunities for microbial conversion were identified. Metagenomic and genome mining approaches were also discussed, as they can provide access to uncultivated or unculturable microorganisms in communal populations and are an unlimited resource for biocatalysts, novel genes and metabolites. Genome mining was seen as an economical approach. The presentation also emphasized that the development of microbial biorefineries would require significant insights into the relevant microorganisms and that biocatalysts were the ultimate in sustainability. In addition, the presentation discussed the natural fibres initiative for biochemicals and biomaterials. Anticipated outputs were identified and work in progress of a new enzyme-retting cocktail to provide diversity and/or consistency in fibre characteristics for various applications were also presented. It was concluded that it is necessary to leverage understanding of biological processes to produce bioproducts in a clean and sustainable manner. tabs., figs.

Seasonal variation in carbon dioxide exchange over a Mediterranean annual grassland in California

Energy Technology Data Exchange (ETDEWEB)

Xu, L; Baldocchi, D

2004-05-01

Understanding how environmental variables affect the processes that regulate the carbon flux over grassland is critical for large-scale modeling research, since grasslands comprise almost one-third of the earth's natural vegetation. To address this issue, fluxes of CO{sub 2} (F{sub c}, flux toward the surface is negative) were measured over a Mediterranean, annual grassland in California, USA for 2 years with the eddy covariance method. To interpret the biotic and abiotic factors that modulate F{sub c} over the course of a year we decomposed net ecosystem CO{sub 2} exchange into its constituent components, ecosystem respiration (R{sub eco}) and gross primary production (GPP). Daytime R{sub eco} was extrapolated from the relationship between temperature and nighttime F{sub c} under high turbulent conditions. Then, GPP was estimated by subtracting daytime values of F{sub c} from daytime estimates of R{sub eco}. Results show that most of carbon exchange, both photosynthesis and respiration, was limited to the wet season (typically from October to mid-May). Seasonal variations in GPP followed closely to changes in leaf area index, which in turn was governed by soil moisture, available sunlight and the timing of the last frost. In general, R{sub eco} was an exponential function of soil temperature, but with season-dependent values of Q{sub 10}. The temperature-dependent respiration model failed immediately after rain events, when large pulses of R{sub eco} were observed. Respiration pulses were especially notable during the dry season when the grass was dead and were the consequence of quickly stimulated microbial activity. Integrated values of GPP, R{sub eco}, and net ecosystem exchange (NEE) were 867, 735, and -132g C m{sup -2}, respectively, for the 2000-2001 season, and 729, 758, and 29g C m{sup -2} for the 2001-2002 season. Thus, the grassland was a moderate carbon sink during the first season and a weak carbon source during the second season. In contrast to a

Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer

Energy Technology Data Exchange (ETDEWEB)

Lin, Xueju; McKinley, James P.; Resch, Charles T.; Kaluzny, Rachael M.; Lauber, C.; Fredrickson, Jim K.; Knight, Robbie C.; Konopka, Allan

2012-03-29

Pyrosequencing analysis of 16S rRNA genes was used to study temporal dynamics of groundwater Bacteria and Archaea over 10 months within 3 well clusters separated by ~30 m and located 250 m from the Columbia River on the Hanford Site, WA. Each cluster contained 3 wells screened at different depths ranging from 10 to 17 m that differed in hydraulic conductivities. Representative samples were selected for analyses of prokaryotic 16S and eukaryotic 18S rRNA gene copy numbers. Temporal changes in community composition occurred in all 9 wells over the 10 month sampling period. However, there were particularly strong effects near the top of the water table when the seasonal rise in the Columbia River caused river water intrusion at the top of the aquifer. The occurrence and disappearance of some microbial assemblages (such as Actinobacteria ACK-M1) were correlated to river water intrusion. This seasonal impact on microbial community structure was greater in the shallow saturated zone than deeper in the aquifer. Spatial and temporal patterns for several 16S rRNA gene operational taxonomic units associated with particular physiological functions (e.g.methane oxidizers and metal reducers) suggests dynamic changes in fluxes of electron donors and acceptors over an annual cycle. In addition, temporal dynamics in eukaryotic 18S rRNA gene copies and the dominance of protozoa in 18S clone libraries suggest that bacterial community dynamics could be affected not only by the physical and chemical environment, but also by top-down biological control.

Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

Directory of Open Access Journals (Sweden)

Darine Trabelsi

2013-01-01

Full Text Available The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

Molecular microbial ecology manual

NARCIS (Netherlands)

Kowalchuk, G.A.; Bruijn, de F.J.; Head, I.M.; Akkermans, A.D.L.

2004-01-01

The field of microbial ecology has been revolutionized in the past two decades by the introduction of molecular methods into the toolbox of the microbial ecologist. This molecular arsenal has helped to unveil the enormity of microbial diversity across the breadth of the earth's ecosystems, and has

Microbial electrosynthetic cells

Energy Technology Data Exchange (ETDEWEB)

May, Harold D.; Marshall, Christopher W.; Labelle, Edward V.

2018-01-30

Methods are provided for microbial electrosynthesis of H.sub.2 and organic compounds such as methane and acetate. Method of producing mature electrosynthetic microbial populations by continuous culture is also provided. Microbial populations produced in accordance with the embodiments as shown to efficiently synthesize H.sub.2, methane and acetate in the presence of CO.sub.2 and a voltage potential. The production of biodegradable and renewable plastics from electricity and carbon dioxide is also disclosed.

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China

Directory of Open Access Journals (Sweden)

C. Zhang

2017-10-01

Full Text Available The nitrate to ammonium ratios in nitrogen (N compounds in wet atmospheric deposits have increased over the recent past, which is a cause for some concern as the individual effects of nitrate and ammonium deposition on the biomass of different soil microbial communities and enzyme activities are still poorly defined. We established a field experiment and applied ammonium (NH4Cl and nitrate (NaNO3 at monthly intervals over a period of 4 years. We collected soil samples from the ammonium and nitrate treatments and control plots in three different seasons, namely spring, summer, and fall, to evaluate the how the biomass of different soil microbial communities and enzyme activities responded to the ammonium (NH4Cl and nitrate (NaNO3 applications. Our results showed that the total contents of phospholipid fatty acids (PLFAs decreased by 24 and 11 % in the ammonium and nitrate treatments, respectively. The inhibitory effects of ammonium on Gram-positive bacteria (G+ and bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi (AMF PLFA contents ranged from 14 to 40 % across the three seasons. We also observed that the absolute activities of C, N, and P hydrolyses and oxidases were inhibited by ammonium and nitrate, but that nitrate had stronger inhibitory effects on the activities of acid phosphatase (AP than ammonium. The activities of N-acquisition specific enzymes (enzyme activities normalized by total PLFA contents were about 21 and 43 % lower in the ammonium and nitrate treatments than in the control, respectively. However, the activities of P-acquisition specific enzymes were about 19 % higher in the ammonium treatment than in the control. Using redundancy analysis (RDA, we found that the measured C, N, and P hydrolysis and polyphenol oxidase (PPO activities were positively correlated with the soil pH and ammonium contents, but were negatively correlated with the nitrate contents. The PLFA biomarker contents were positively

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China

Science.gov (United States)

Zhang, Chuang; Zhang, Xin-Yu; Zou, Hong-Tao; Kou, Liang; Yang, Yang; Wen, Xue-Fa; Li, Sheng-Gong; Wang, Hui-Min; Sun, Xiao-Min

2017-10-01

The nitrate to ammonium ratios in nitrogen (N) compounds in wet atmospheric deposits have increased over the recent past, which is a cause for some concern as the individual effects of nitrate and ammonium deposition on the biomass of different soil microbial communities and enzyme activities are still poorly defined. We established a field experiment and applied ammonium (NH4Cl) and nitrate (NaNO3) at monthly intervals over a period of 4 years. We collected soil samples from the ammonium and nitrate treatments and control plots in three different seasons, namely spring, summer, and fall, to evaluate the how the biomass of different soil microbial communities and enzyme activities responded to the ammonium (NH4Cl) and nitrate (NaNO3) applications. Our results showed that the total contents of phospholipid fatty acids (PLFAs) decreased by 24 and 11 % in the ammonium and nitrate treatments, respectively. The inhibitory effects of ammonium on Gram-positive bacteria (G+) and bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi (AMF) PLFA contents ranged from 14 to 40 % across the three seasons. We also observed that the absolute activities of C, N, and P hydrolyses and oxidases were inhibited by ammonium and nitrate, but that nitrate had stronger inhibitory effects on the activities of acid phosphatase (AP) than ammonium. The activities of N-acquisition specific enzymes (enzyme activities normalized by total PLFA contents) were about 21 and 43 % lower in the ammonium and nitrate treatments than in the control, respectively. However, the activities of P-acquisition specific enzymes were about 19 % higher in the ammonium treatment than in the control. Using redundancy analysis (RDA), we found that the measured C, N, and P hydrolysis and polyphenol oxidase (PPO) activities were positively correlated with the soil pH and ammonium contents, but were negatively correlated with the nitrate contents. The PLFA biomarker contents were positively correlated with soil

Wet season cyanobacterial N enrichment highly correlated with species richness and Nostoc in the northern Australian savannah

Science.gov (United States)

Williams, Wendy; Büdel, Burkhard; Williams, Stephen

2018-04-01

The Boodjamulla National Park research station is situated in the north-western Queensland dry savannah, where the climate is dominated by summer monsoons and virtually dry winters. Under shrub canopies and in between the tussock grasses cyanobacterial crusts almost entirely cover the flood plain soil surfaces. Seasonality drives N fixation, and in the savannah this has a large impact on both plant and soil function. Many cyanobacteria fix dinitrogen that is liberated into the soil in both inorganic and organic N forms. We examined cyanobacterial species richness and bioavailable N spanning 7 months of a typical wet season. Over the wet season cyanobacterial richness ranged from 6 to 19 species. N-fixing Scytonema accounted for seasonal averages between 51 and 93 % of the biocrust. Cyanobacterial richness was highly correlated with N fixation and bioavailable N in 0-1 cm. Key N-fixing species such as Nostoc, Symploca and Gloeocapsa significantly enriched soil N although Nostoc was the most influential. Total seasonal N fixation by cyanobacteria demonstrated the variability in productivity according to the number of wet days as well as the follow-on days where the soil retained adequate moisture. Based on total active days per month we estimated that N soil enrichment via cyanobacteria would be ˜ 5.2 kg ha-1 annually which is comparable to global averages. This is a substantial contribution to the nutrient-deficient savannah soils that are almost entirely reliant on the wet season for microbial turnover of organic matter. Such well-defined seasonal trends and synchronisation in cyanobacterial species richness, N fixation, bioavailable N and C fixation (Büdel et al., 2018) provide important contributions to multifunctional microprocesses and soil fertility.

Microbial Energy Conversion

Energy Technology Data Exchange (ETDEWEB)

Buckley, Merry [American Society for Microbiology (ASM), Washington, DC (United States); Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

2006-10-01

The American Academy of Microbiology convened a colloquium March 10-12, 2006, in San Francisco, California, to discuss the production of energy fuels by microbial conversions. The status of research into various microbial energy technologies, the advantages and disadvantages of each of these approaches, research needs in the field, and education and training issues were examined, with the goal of identifying routes for producing biofuels that would both decrease the need for fossil fuels and reduce greenhouse gas emissions. Currently, the choices for providing energy are limited. Policy makers and the research community must begin to pursue a broader array of potential energy technologies. A diverse energy portfolio that includes an assortment of microbial energy choices will allow communities and consumers to select the best energy solution for their own particular needs. Funding agencies and governments alike need to prepare for future energy needs by investing both in the microbial energy technologies that work today and in the untested technologies that will serve the world’s needs tomorrow. More mature bioprocesses, such as ethanol production from starchy materials and methane from waste digestors, will find applications in the short term. However, innovative techniques for liquid fuel or biohydrogen production are among the longer term possibilities that should also be vigorously explored, starting now. Microorganisms can help meet human energy needs in any of a number of ways. In their most obvious role in energy conversion, microorganisms can generate fuels, including ethanol, hydrogen, methane, lipids, and butanol, which can be burned to produce energy. Alternatively, bacteria can be put to use in microbial fuel cells, where they carry out the direct conversion of biomass into electricity. Microorganisms may also be used some day to make oil and natural gas technologies more efficient by sequestering carbon or by assisting in the recovery of oil and

Substitution of soybean meal for cottonseed meal in multiple supplements for grazing beef heifers in the dry season

Directory of Open Access Journals (Sweden)

Román Maza Ortega

2016-02-01

Full Text Available The objective of this study was to evaluate the effect of substituting soybean meal for cottonseed meal in multiple supplements on the nutritional characteristics and performance of beef heifers in their postweaning phase on Brachiaria decumbens pastures during the dry season. Twenty-four Nellore beef heifers (average initial age and weight of 8 mo and 210±6 kg, respectively were used. The design was completely randomized, with four treatments and six replicates. Supplements contained approximately 30% crude protein (CP and a progressive substitution of soybean meal for cottonseed meal (0, 50 and 100%. The control animals received only a mineral mixture ad libitum, and those on the other treatments received supplementation at 1.0 kg/animal/day. No differences were found in ADG between supplemented and control animals (P>0.10. Supplementation increased crude protein (CP intake only (P<0.10. The level of substitution of soybean meal for cottonseed meal did not affect (P>0.10 the intake of supplemented animals. Supplementation elevated the apparent digestibility coefficients (P<0.10 of OM, CP, NFC and TDN, but not EE or NDFap (P>0.10. A positive linear effect (P<0.10 of the level of substitution of soybean meal for cottonseed cake was observed on the digestibility of OM, NFC and TDN. Supplementation and the level of substitution had an effect (P<0.10 on the serum urea nitrogen and urine urea nitrogen contents. Supplementation or substitution level had no effect on the flow of microbial nitrogen to the intestine (MICN or efficiency of microbial protein synthesis (EMPS (P>0.10. Substitution caused a decreasing linear effect (P<0.10 on microbial nitrogen/nitrogen intake ratio (MICNR. In conclusion, substitution of soybean meal for cottonseed meal in multiple supplements during the dry season does not impair the productive performance of beef heifers.

Microbial bioinformatics 2020.

Science.gov (United States)

Pallen, Mark J

2016-09-01

Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Effects of land use change and seasonality of precipitation on soil nitrogen in a dry tropical forest area in the Western Llanos of Venezuela.

Science.gov (United States)

González-Pedraza, Ana Francisca; Dezzeo, Nelda

2014-01-01

We evaluated changes of different soil nitrogen forms (total N, available ammonium and nitrate, total N in microbial biomass, and soil N mineralization) after conversion of semideciduous dry tropical forest in 5- and 18-year-old pastures (YP and OP, resp.) in the western Llanos of Venezuela. This evaluation was made at early rainy season, at end rainy season, and during dry season. With few exceptions, no significant differences were detected in the total N in the three study sites. Compared to forest soils, YP showed ammonium losses from 4.2 to 62.9% and nitrate losses from 20.0 to 77.8%, depending on the season of the year. In OP, the ammonium content increased from 50.0 to 69.0% at the end of the rainy season and decreased during the dry season between 25.0 and 55.5%, whereas the nitrate content increased significantly at early rainy season. The net mineralization and the potentially mineralizable N were significantly higher (P forest and YP, which would indicate a better quality of the substrate in OP for mineralization. The mineralization rate constant was higher in YP than in forest and OP. This could be associated with a reduced capacity of these soils to preserve the available nitrogen.

Long-term spatial and temporal microbial community dynamics in a large-scale drinking water distribution system with multiple disinfectant regimes.

Science.gov (United States)

Potgieter, Sarah; Pinto, Ameet; Sigudu, Makhosazana; du Preez, Hein; Ncube, Esper; Venter, Stephanus

2018-08-01

Long-term spatial-temporal investigations of microbial dynamics in full-scale drinking water distribution systems are scarce. These investigations can reveal the process, infrastructure, and environmental factors that influence the microbial community, offering opportunities to re-think microbial management in drinking water systems. Often, these insights are missed or are unreliable in short-term studies, which are impacted by stochastic variabilities inherent to large full-scale systems. In this two-year study, we investigated the spatial and temporal dynamics of the microbial community in a large, full scale South African drinking water distribution system that uses three successive disinfection strategies (i.e. chlorination, chloramination and hypochlorination). Monthly bulk water samples were collected from the outlet of the treatment plant and from 17 points in the distribution system spanning nearly 150 km and the bacterial community composition was characterised by Illumina MiSeq sequencing of the V4 hypervariable region of the 16S rRNA gene. Like previous studies, Alpha- and Betaproteobacteria dominated the drinking water bacterial communities, with an increase in Betaproteobacteria post-chloramination. In contrast with previous reports, the observed richness, diversity, and evenness of the bacterial communities were higher in the winter months as opposed to the summer months in this study. In addition to temperature effects, the seasonal variations were also likely to be influenced by changes in average water age in the distribution system and corresponding changes in disinfectant residual concentrations. Spatial dynamics of the bacterial communities indicated distance decay, with bacterial communities becoming increasingly dissimilar with increasing distance between sampling locations. These spatial effects dampened the temporal changes in the bulk water community and were the dominant factor when considering the entire distribution system. However

Seasonal variation of monomethylmercury concentrations in surface sediments of the Tagus Estuary (Portugal)

International Nuclear Information System (INIS)

Canario, Joao; Branco, Vasco; Vale, Carlos

2007-01-01

Surface sediments (0-2 cm) were collected at 40 sites along the Tagus Estuary in July and December 2004. The sediments were analysed for total mercury, monomethylmercury (MMHg) and interpretative parameters (e.g. redox potential, pH, C org ). No significant differences in total Hg, pH, Al, Fe, Mn and C org were found between sediments collected in the two periods, but MMHg concentrations were higher in July. On average sediments were warmer and more reducing in summer. On the basis of these results, an increase of 7 kg of MMHg (+37%) in surface sediments of the Tagus Estuary was estimated. Presumably higher temperatures in summer promote the increase of microbial activity and higher methylation rates. The alterations observed in this study point to the potential importance of seasonal changes in MMHg production at surface sediments with eventual changes in the MMHg uptake by benthic invertebrates and other organisms in the food web. - Seasonal changes in monomethylmercury production in sediments may increase its uptake by benthic invertebrates and other organisms in the food web

11 Soil Microbial Biomass

African Journals Online (AJOL)

186–198. Insam H. (1990). Are the soil microbial biomass and basal respiration governed by the climatic regime? Soil. Biol. Biochem. 22: 525–532. Insam H. D. and Domsch K. H. (1989). Influence of microclimate on soil microbial biomass. Soil Biol. Biochem. 21: 211–21. Jenkinson D. S. (1988). Determination of microbial.

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

Science.gov (United States)

Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

2013-01-01

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

Energy Technology Data Exchange (ETDEWEB)

White, G.J.

1996-08-01

Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus is on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.

Microbial properties explain temporal variation in soil respiration in a grassland subjected to nitrogen addition

Science.gov (United States)

Li, Yue; Liu, Yinghui; Wu, Shanmei; Niu, Lei; Tian, Yuqiang

2015-01-01

The role of soil microbial variables in shaping the temporal variability of soil respiration has been well acknowledged but is poorly understood, particularly under elevated nitrogen (N) deposition conditions. We measured soil respiration along with soil microbial properties during the early, middle, and late growing seasons in temperate grassland plots that had been treated with N additions of 0, 2, 4, 8, 16, or 32 g N m−2 yr−1 for 10 years. Representing the averages over three observation periods, total (Rs) and heterotrophic (Rh) respiration were highest with 4 g N m−2 yr−1, but autotrophic respiration (Ra) was highest with 8 to 16 g N m−2 yr−1. Also, the responses of Rh and Ra were unsynchronized considering the periods separately. N addition had no significant impact on the temperature sensitivity (Q10) for Rs but inhibited the Q10 for Rh. Significant interactions between observation period and N level occurred in soil respiration components, and the temporal variations in soil respiration components were mostly associated with changes in microbial biomass carbon (MBC) and phospholipid fatty acids (PLFAs). Further observation on soil organic carbon and root biomass is needed to reveal the long-term effect of N deposition on soil C sequestration. PMID:26678303

Wet season cyanobacterial N enrichment highly correlated with species richness and Nostoc in the northern Australian savannah

Directory of Open Access Journals (Sweden)

W. Williams

2018-04-01

Full Text Available The Boodjamulla National Park research station is situated in the north-western Queensland dry savannah, where the climate is dominated by summer monsoons and virtually dry winters. Under shrub canopies and in between the tussock grasses cyanobacterial crusts almost entirely cover the flood plain soil surfaces. Seasonality drives N fixation, and in the savannah this has a large impact on both plant and soil function. Many cyanobacteria fix dinitrogen that is liberated into the soil in both inorganic and organic N forms. We examined cyanobacterial species richness and bioavailable N spanning 7 months of a typical wet season. Over the wet season cyanobacterial richness ranged from 6 to 19 species. N-fixing Scytonema accounted for seasonal averages between 51 and 93 % of the biocrust. Cyanobacterial richness was highly correlated with N fixation and bioavailable N in 0–1 cm. Key N-fixing species such as Nostoc, Symploca and Gloeocapsa significantly enriched soil N although Nostoc was the most influential. Total seasonal N fixation by cyanobacteria demonstrated the variability in productivity according to the number of wet days as well as the follow-on days where the soil retained adequate moisture. Based on total active days per month we estimated that N soil enrichment via cyanobacteria would be  ∼  5.2 kg ha−1 annually which is comparable to global averages. This is a substantial contribution to the nutrient-deficient savannah soils that are almost entirely reliant on the wet season for microbial turnover of organic matter. Such well-defined seasonal trends and synchronisation in cyanobacterial species richness, N fixation, bioavailable N and C fixation (Büdel et al., 2018 provide important contributions to multifunctional microprocesses and soil fertility.

Molecular characteristics of Clostridium difficile strains from patients with a first recurrence more than 8 weeks after the primary infection.

Science.gov (United States)

Chen, Yijian; Rashid, Mamun Ur; Huang, Haihui; Fang, Hong; Nord, Carl Erik; Wang, Minggui; Weintraub, Andrej

2017-08-01

Nearly all published studies of recurrent Clostridium difficile infections (CDI) report recurrent CDI within 8 weeks after the primary infection. This study explored the molecular characteristics of C. difficile isolates from the first recurrent CDI more than 8 weeks after the primary infection. Consecutive hospitalized patients with a recurrent CDI more than 8 weeks after a primary infection were enrolled prospectively from January 2008 to February 2011. All C. difficile isolates of the primary and recurrent infections were collected and subjected to polymerase chain reaction ribotyping and antimicrobial susceptibility testing. There were 62 cases of CDI in this study, which included 32 cases (51.6%) of recurrence due to the same ribotype of C. difficile, 26 (41.9%) cases due to a different ribotype, and four (6.5%) cases with 2-4 recurrences due to the same or different strains. One hundred and forty C. difficile isolates were obtained, which included 62 primary CDI isolates and 78 recurrent isolates. Ribotype 020 was the most common C. difficile strain in primary and recurrent infections. Ribotype 001 accounted for 15.4% (10/78) of recurrent infections and 3.2% (2/62) of primary infections (p = 0.0447). The minimum inhibitory concentration at 90% (MIC 90 ) values of linezolid, moxifloxacin, and clindamycin against type 001 strains were much higher, compared to the three other common ribotypes. Recurrent CDI more than 8 weeks after a primary infection can be caused by the same or different C. difficile ribotype at similar percentages. Ribotype 001 C. difficile strains, which have a lower susceptibility to antimicrobials, were isolated more frequently in patients with a recurrent CDI. Copyright © 2015. Published by Elsevier B.V.

Seasonal dynamics of dissolved, particulate and microbial components of a tidal saltmarsh-dominated estuary under contrasting levels of freshwater discharge

Science.gov (United States)

Bittar, Thais B.; Berger, Stella A.; Birsa, Laura M.; Walters, Tina L.; Thompson, Megan E.; Spencer, Robert G. M.; Mann, Elizabeth L.; Stubbins, Aron; Frischer, Marc E.; Brandes, Jay A.

2016-12-01

Tidal Spartina-dominated saltmarshes and estuaries on the Southeast US coast are global hotspots of productivity. In coastal Georgia, tidal amplitudes and saltmarsh productivity are the highest along the Southeast US coast. Coastal Georgia is characterized by a humid subtropical seasonal climate, and inter-annual variability in precipitation, and freshwater discharge. The 2012-2013 timeframe encompassed contrasting levels of discharge for the Savannah River, a major Georgia river, with a 4.3-fold greater discharge in summer 2013 relative to summer 2012. In situ measurements of temperature, salinity, precipitation and Secchi depth, and water samples were collected weekly at high tide throughout 2012 and 2013 from the Skidaway River Estuary, a tidal saltmarsh-dominated estuary in coastal Georgia influenced by Savannah River hydrology. The effects of elevated discharge on the seasonal trends of water column components were evaluated. The shift from low discharge (2012) to high discharge (2013) led to decreased salinity in summer 2013, but no significant increases in inorganic nutrient (NH4, NOx, SiO2 and PO4) concentrations. Dissolved inorganic carbon (DIC) concentrations decreased, and DIC stable isotopic signatures (δ13C-DIC values) were depleted in summer 2013 relative to summer 2012. In 2013 dissolved organic carbon (DOC) concentrations, chromophoric and fluorescent dissolved organic matter (DOM: CDOM, FDOM) intensities, specific UV-absorbance (SUVA254) and relative humic-like fluorescence were all higher than in 2012, indicating that, as discharge increased in 2013, estuarine water became enriched in terrigenous DOM. Secchi depth and particulate organic carbon (POC) and nitrogen (PON) concentrations displayed clear seasonal patterns that were not significantly altered by discharge. However, δ13C-POC and δ15N-PON isotopic signatures indicated higher terrigenous contributions at elevated discharge. Discharge influenced cyanobacterial composition, but did not

Impacts of Antibiotic and Bacteriophage Treatments on the Gut-Symbiont-Associated Blissus insularis (Hemiptera: Blissidae

Directory of Open Access Journals (Sweden)

Yao Xu

2016-11-01

Full Text Available The Southern chinch bug, Blissus insularis, possesses specialized midgut crypts that harbor dense populations of the exocellular symbiont Burkholderia. Oral administration of antibiotics suppressed the gut symbionts in B. insularis and negatively impacted insect host fitness, as reflected by retarded development, smaller body size, and higher susceptibility to an insecticide, bifenthrin. Considering that the antibiotics probably had non-lethal but toxic effects on host fitness, attempts were conducted to reduce gut symbionts using bacteriophage treatment. Soil-lytic phages active against the cultures of specific Burkholderia ribotypes were successfully isolated using a soil enrichment protocol. Characterization of the BiBurk16MC_R phage determined its specificity to the Bi16MC_R_vitro ribotype and placed it within the family Podoviridae. Oral administration of phages to fifth-instar B. insularis, inoculated with Bi16MC_R_vitro as neonates had no deleterious effects on host fitness. However, the ingested phages failed to impact the crypt-associated Burkholderia. The observed inactivity of the phage was likely due to the blockage of the connection between the anterior and posterior midgut regions. These findings suggest that the initial colonization by Burkholderia programs the ontogeny of the midgut, providing a sheltered residence protected from microbial antagonists.

Out-of-season recollection of drug use for seasonal IgE-mediated rhinitis

DEFF Research Database (Denmark)

Bødtger, Uffe; Malling, Hans-Jørgen; Poulsen, Lars K

2005-01-01

in a double-blind study. Drug use was recorded daily during the season 2000 and out-seasonally 6 months after the seasons 1999 and 2000. The mean daily drug use was transformed into a 4-point categorical scale for simplicity and was calculated for the out-seasonal rating and for 6 in-seasonal periods...

Photochemical and microbial alterations of DOM spectroscopic properties in the estuarine system Ria de Aveiro.

Science.gov (United States)

Santos, L; Santos, E B H; Dias, J M; Cunha, A; Almeida, A

2014-08-01

The influence of photochemical transformations of chromophoric dissolved organic matter (CDOM) on microbial communities was evaluated in the estuarine system Ria de Aveiro. Two sites, representative of the marine and brackish water zones of the estuary, were surveyed regularly in order to determine seasonal and vertical profiles of variation of CDOM properties. Optical parameters of CDOM indicative of aromaticity and molecular weight were used to establish CDOM sources, and microbial abundance and activity was characterized. Additionally, microcosm experiments were performed in order to simulate photochemical reactions of CDOM and to evaluate microbial responses to light-induced changes in CDOM composition. The CDOM of the two estuarine zones showed different spectral characteristics, with significantly higher values of the specific ultra-violet absorbance at 254 nm (SUVA254) (5.5 times) and of the absorption coefficient at 350 nm (a350) (12 times) and lower SR (S275-295/S350-400) ratio at brackish water compared with the marine zone, reflecting the different amounts and prevailing sources of organic matter, as well as distinct riverine and oceanic influences. At the marine zone, the abundance of bacteria and the activity of Leu-AMPase correlated with a350 and a254, suggesting a microbial contribution to the HMW CDOM pool. The irradiation of DOM resulted in a decrease of the values of a254 and a350 and an increase of the slope S275-295 and of the ratios E2 : E3 (a250/a365) and SR, which in turn increase its bioavailability. However, the extent of photoinduced transformations and microbial responses was dependent on the initial optical characteristics of CDOM. In Ria de Aveiro both photochemical and microbial processes yielded optical changes in CDOM and the overall results of these combined processes determine the fate of CDOM in the estuarine system and have an influence on local productivity and in adjacent coastal areas.

Biotechnological Aspects of Microbial Extracellular Electron Transfer

Science.gov (United States)

Kato, Souichiro

2015-01-01

Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

A theoretical reassessment of microbial maintenance and implications for microbial ecology modeling.

Science.gov (United States)

Wang, Gangsheng; Post, Wilfred M

2012-09-01

We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a theoretical reassessment. We provided a rigorous proof that the true growth yield coefficient (Y(G)) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert (μ(max,H)) is higher than those in the other two models (μ(max,P) and μ(max,C)), and the difference is the physiological maintenance factor (m(q) = a); and (3) the overall maintenance coefficient (m(T)) is more sensitive to m(q) than to the specific growth rate (μ(G)) and Y(G). Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models. © This article is a US government work and is in the public domain in the USA.

Pesticide residues and microbial contamination of water resources in the MUDA rice agroecosystem

International Nuclear Information System (INIS)

Cheah Uan Boh; Lum Keng Yeang

2002-01-01

Studies on the water resources of the Muda rice growing areas revealed evidence of pesticide residues in the agroecosystem. While the cyclodiene endosulfan was found as a ubiquitous contaminant, the occurrence of other organochlorine insecticides was sporadic. The presence of 2,4-D, paraquat and molinate residues was also evident but the occurrence of these herbicides was seasonal. Residue levels of molinate were generally higher than those from the other herbicides. The problem of thiobencarb and carbofuran residues was not encountered. Analyses for microbial contamination revealed that the water resources were unfit for drinking; coliform counts were higher during certain periods of the year than others. (Author)

Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica

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Bradley M. Tebo

2015-03-01

Full Text Available The Earth’s crust hosts a subsurface, dark, and oligotrophic biosphere that is poorly understood in terms of the energy supporting its biomass production and impact on food webs at the Earth’s surface. Dark oligotrophic volcanic ecosystems (DOVEs are good environments for investigations of life in the absence of sunlight as they are poor in organics, rich in chemical reactants and well known for chemical exchange with Earth’s surface systems. Ice caves near the summit of Mt. Erebus (Antarctica offer DOVEs in a polar alpine environment that is starved in organics and with oxygenated hydrothermal circulation in highly reducing host rock. We surveyed the microbial communities using PCR, cloning, sequencing and analysis of the small subunit (16S ribosomal and Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (RubisCO genes in sediment samples from three different caves, two that are completely dark and one that receives snow-filtered sunlight seasonally. The microbial communities in all three caves are composed primarily of Bacteria and fungi; Archaea were not detected. The bacterial communities from these ice caves display low phylogenetic diversity, but with a remarkable diversity of RubisCO genes including new deeply branching Form I clades, implicating the Calvin-Benson-Bassham cycle as a pathway of CO2 fixation. The microbial communities in one of the dark caves, Warren Cave, which has a remarkably low phylogenetic diversity, were analyzed in more detail to gain a possible perspective on the energetic basis of the microbial ecosystem in the cave. Atmospheric carbon (CO2 and CO, including from volcanic emissions, likely supplies carbon and/or some of the energy requirements of chemoautotrophic microbial communities in Warren Cave and probably other Mt. Erebus ice caves. Our work casts a first glimpse at Mt. Erebus ice caves as natural laboratories for exploring carbon, energy and nutrient sources in the subsurface biosphere and the

The Microbial DNA Index System (MiDIS): A tool for microbial pathogen source identification

Energy Technology Data Exchange (ETDEWEB)

Velsko, S. P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2010-08-09

The microbial DNA Index System (MiDIS) is a concept for a microbial forensic database and investigative decision support system that can be used to help investigators identify the sources of microbial agents that have been used in a criminal or terrorist incident. The heart of the proposed system is a rigorous method for calculating source probabilities by using certain fundamental sampling distributions associated with the propagation and mutation of microbes on disease transmission networks. This formalism has a close relationship to mitochondrial and Y-chromosomal human DNA forensics, and the proposed decision support system is somewhat analogous to the CODIS and SWGDAM mtDNA databases. The MiDIS concept does not involve the use of opportunistic collections of microbial isolates and phylogenetic tree building as a basis for inference. A staged approach can be used to build MiDIS as an enduring capability, beginning with a pilot demonstration program that must meet user expectations for performance and validation before evolving into a continuing effort. Because MiDIS requires input from a a broad array of expertise including outbreak surveillance, field microbial isolate collection, microbial genome sequencing, disease transmission networks, and laboratory mutation rate studies, it will be necessary to assemble a national multi-laboratory team to develop such a system. The MiDIS effort would lend direction and focus to the national microbial genetics research program for microbial forensics, and would provide an appropriate forensic framework for interfacing to future national and international disease surveillance efforts.

Effects of Elevated Carbon Dioxide and Salinity on the Microbial Diversity in Lithifying Microbial Mats

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Steven R. Ahrendt

2014-03-01

Full Text Available Atmospheric levels of carbon dioxide (CO2 are rising at an accelerated rate resulting in changes in the pH and carbonate chemistry of the world’s oceans. However, there is uncertainty regarding the impact these changing environmental conditions have on carbonate-depositing microbial communities. Here, we examine the effects of elevated CO2, three times that of current atmospheric levels, on the microbial diversity associated with lithifying microbial mats. Lithifying microbial mats are complex ecosystems that facilitate the trapping and binding of sediments, and/or the precipitation of calcium carbonate into organosedimentary structures known as microbialites. To examine the impact of rising CO2 and resulting shifts in pH on lithifying microbial mats, we constructed growth chambers that could continually manipulate and monitor the mat environment. The microbial diversity of the various treatments was compared using 16S rRNA gene pyrosequencing. The results indicated that elevated CO2 levels during the six month exposure did not profoundly alter the microbial diversity, community structure, or carbonate precipitation in the microbial mats; however some key taxa, such as the sulfate-reducing bacteria Deltasulfobacterales, were enriched. These results suggest that some carbonate depositing ecosystems, such as the microbialites, may be more resilient to anthropogenic-induced environmental change than previously thought.

Seasonal prolactin secretion and its role in seasonal reproduction: a review.

Science.gov (United States)

Curlewis, J D

1992-01-01

The majority of seasonally breeding mammals show a seasonal pattern of prolactin secretion with peak concentrations in spring or summer and a nadir in autumn or winter. Photoperiod influences prolactin secretion via its effects on the secretion of the pineal hormone melatonin. Preliminary evidence suggests that the effects of melatonin on both prolactin and gonadotrophin secretion are via a common target area, possibly within the anterior hypothalamus, and that differences in response to photoperiod may be due to differences in the processing and/or interpretation of the melatonin signal. In contrast to seasonal gonadotrophin secretion, the seasonal changes in prolactin are not due to changes in the sensitivity of a feedback loop and so must be due to direct effects on the hypothalamic pathways that control prolactin secretion. Little else can be said with confidence about the neuroendocrine mechanisms that lead to the seasonal changes in prolactin secretion. Dopamine and noradrenaline turnover in the arcuate nucleus and median eminence decrease under short daylength. If catecholamine turnover in these structures is positively correlated with catecholamine concentrations in the long or short hypophysial portal vessels, it is unlikely that the decrease in prolactin concentration in winter is due to the effects of increased concentrations of dopamine or noradrenaline in the portal vessels. There is, however, evidence for increased pituitary sensitivity to dopamine under short daylength, so increased dopamine concentrations may not be required for suppression of prolactin secretion at this time. In addition to the diminished secretion of prolactin under short daylength, rate of prolactin synthesis and pituitary content of prolactin also decline although the mechanisms that regulate these changes are poorly understood. Although all seasonal breeders show a seasonal change in prolactin secretion, there are continuously breeding species in which prolactin secretion is

MICROBIAL FUEL CELL

DEFF Research Database (Denmark)

2008-01-01

A novel microbial fuel cell construction for the generation of electrical energy. The microbial fuel cell comprises: (i) an anode electrode, (ii) a cathode chamber, said cathode chamber comprising an in let through which an influent enters the cathode chamber, an outlet through which an effluent...

Molecular ecology of microbial mats

NARCIS (Netherlands)

Bolhuis, H.; Cretoiu, M.S.; Stal, L.J.

2014-01-01

Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep

Diphtheria in the Republic of Georgia: Use of Molecular Typing Techniques for Characterization of Corynebacterium diphtheriae Strains

Science.gov (United States)

Sulakvelidze, Alexander; Kekelidze, Merab; Gomelauri, Tsaro; Deng, Yingkang; Khetsuriani, Nino; Kobaidze, Ketino; De Zoysa, Aruni; Efstratiou, Androulla; Morris, J. Glenn; Imnadze, Paata

1999-01-01

Sixty-six Corynebacterium diphtheriae strains (62 of the gravis biotype and 4 of the mitis biotype) isolated during the Georgian diphtheria epidemic of 1993 to 1998 and 13 non-Georgian C. diphtheriae strains (10 Russian and 3 reference isolates) were characterized by (i) biotyping, (ii) toxigenicity testing with the Elek assay and PCR, (iii) the randomly amplified polymorphic DNA (RAPD) technique, and (iv) pulsed-field gel electrophoresis (PFGE). Fifteen selected strains were ribotyped. Six RAPD types and 15 PFGE patterns were identified among all strains examined, and 12 ribotypes were found among the 15 strains that were ribotyped. The Georgian epidemic apparently was caused by one major clonal group of C. diphtheriae (PFGE type A, ribotype R1), which was identical to the predominant epidemic strain(s) isolated during the concurrent diphtheria epidemic in Russia. A dendrogram based on the PFGE patterns revealed profound differences between the minor (nonpredominant) epidemic strains found in Georgia and Russia. The methodologies for RAPD typing, ribotyping, and PFGE typing of C. diphtheriae strains were improved to enable rapid and convenient molecular typing of the strains. The RAPD technique was adequate for biotype differentiation; however, PFGE and ribotyping were better (and equal to each other) at discriminating between epidemiologically related and unrelated isolates. PMID:10488190

Changing Seasonality and the Role of the Shoulder Season - Evidence from Denamrk

DEFF Research Database (Denmark)

Sørensen, Nils Karl

2009-01-01

the issue of the shoulder season in a time series framework. Departing from a discussion of the nature of types of seasonal variation, a test is set up in order to examine the impact of the shoulder season. The test examines the impact on the mean share of hotel nights in the shoulder season months in two...

Microbial biosensors for environmental monitoring

Directory of Open Access Journals (Sweden)

David VOGRINC

2015-12-01

Full Text Available Microbial biosensors are analytical devices capable of sensing substances in the environment due to the specific biological reaction of the microorganism or its parts. Construction of a microbial biosensor requires knowledge of microbial response to the specific analyte. Linking this response with the quantitative data, using a transducer, is the crucial step in the construction of a biosensor. Regarding the transducer type, biosensors are divided into electrochemical, optical biosensors and microbial fuel cells. The use of the proper configuration depends on the selection of the biosensing element. With the use of transgenic E. coli strains, bioluminescence or fluorescence based biosensors were developed. Microbial fuel cells enable the use of the heterogeneous microbial populations, isolated from wastewater. Different microorganisms are used for different pollutants – pesticides, heavy metals, phenolic compounds, organic waste, etc. Biosensing enables measurement of their concentration and their toxic or genotoxic effects on the microbes. Increasing environmental awareness has contributed to the increase of interest for biomonitoring. Although technologies, such as bioinformatics and genetic engineering, allow us to design complex and efficient microbial biosensors for environmental pollutants, the transfer of the laboratory work to the field still remains a problem to solve.

Seasonal dynamics in colored dissolved organic matter in the Mediterranean Sea: Patterns and drivers

Science.gov (United States)

Xing, Xiaogang; Claustre, Hervé; Wang, Haili; Poteau, Antoine; D`Ortenzio, Fabrizio

2014-01-01

Two autonomous profiling “Bio-Argo” floats were deployed in the northwestern and eastern sub-basins of the Mediterranean Sea in 2008. They recorded at high vertical (1 m) and temporal (5 day) resolution, the vertical distribution and seasonal variation of colored dissolved organic matter (CDOM), as well as of chlorophyll-a concentration and hydrological variables. The CDOM standing stock presented a clear seasonal dynamics with the progressive summer formation and winter destruction of subsurface CDOM maxima (YSM, for Yellow Substance Maximum). It was argued that subsurface CDOM is a by-product of phytoplankton, based on two main characteristics, (1) the YSM was located at the same depth than the deep chlorophyll maximum (DCM) and (2) the CDOM increased in summer parallels the decline in chlorophyll-a. These observations suggested an indirect but tight coupling between subsurface CDOM and phytoplankton via microbial activity or planktonic foodweb interactions. Moreover, the surface CDOM variations observed both by floats and MODIS displayed different seasonal dynamics from what recorded at subsurface one. This implies that CDOM standing stock can be hardly detected by satellite. It is worthnoting that surface CDOM was found to be more related to the sea surface temperature (SST) than chlorophyll-a concentration, suggesting its physical origin, in contrast to the biological origin of YSM and subsurface standing stocks.

Experimental drought induces short-term changes in soil functionality and microbial community structure after fire in a Mediterranean shrubland

Science.gov (United States)

Hinojosa, M. B.; Parra, A.; Laudicina, V. A.; Moreno, J. M.

2014-10-01

Fire is a major ecosystem driver, causing significant changes in soil nutrients and microbial community structure and functionality. Post-fire soil dynamics can vary depending on rainfall patterns, although variations in response to drought are poorly known. This is particularly important in areas with poor soils and limited rainfall, like arid and semiarid ones. Furthermore, climate change projections in many such areas anticipate reduced precipitation and longer drought, together with an increase in fire severity. The effects of experimental drought and fire were studied on soils in a Mediterranean Cistus-Erica shrubland in Central Spain. A replicated (n = 4) field experiment was carried out in which four levels of rainfall pattern were implemented by means of a rain-out shelters and irrigation system. The treatments were: environmental control (natural rainfall), historical control (long-term average rainfall, 2 months drought), moderate drought (25% reduction of historical control, 5 months drought) and severe drought (45% reduction, 7 months drought). After one growing season, the plots were burned with high fire intensity, except a set of unburned plots that served as control. Soils were collected seasonally during one year and variables related to soil nutrient availability and microbial community structure and functionality were studied. Burned soils increased nutrient availability (P, N, K) with respect to unburned ones, but drought reduced such an increase in P, while it further increased N and K. Such changes in available soil nutrients were short-lived. Drought caused a further decrease of enzyme activities, carbon mineralization rate and microbial biomass. Fire decreased the relative abundance of fungi and actinomycetes. However, fire and drought caused a further reduction in fungi, with bacteria becoming relatively more abundant. Arguably, increasing drought and fires due to climate change will likely shift soil recovery after fire.

Small mammal use of native warm-season and non-native cool-season grass forage fields

Science.gov (United States)

Ryan L Klimstra,; Christopher E Moorman,; Converse, Sarah J.; Royle, J. Andrew; Craig A Harper,

2015-01-01

Recent emphasis has been put on establishing native warm-season grasses for forage production because it is thought native warm-season grasses provide higher quality wildlife habitat than do non-native cool-season grasses. However, it is not clear whether native warm-season grass fields provide better resources for small mammals than currently are available in non-native cool-season grass forage production fields. We developed a hierarchical spatially explicit capture-recapture model to compare abundance of hispid cotton rats (Sigmodon hispidus), white-footed mice (Peromyscus leucopus), and house mice (Mus musculus) among 4 hayed non-native cool-season grass fields, 4 hayed native warm-season grass fields, and 4 native warm-season grass-forb ("wildlife") fields managed for wildlife during 2 summer trapping periods in 2009 and 2010 of the western piedmont of North Carolina, USA. Cotton rat abundance estimates were greater in wildlife fields than in native warm-season grass and non-native cool-season grass fields and greater in native warm-season grass fields than in non-native cool-season grass fields. Abundances of white-footed mouse and house mouse populations were lower in wildlife fields than in native warm-season grass and non-native cool-season grass fields, but the abundances were not different between the native warm-season grass and non-native cool-season grass fields. Lack of cover following haying in non-native cool-season grass and native warm-season grass fields likely was the key factor limiting small mammal abundance, especially cotton rats, in forage fields. Retention of vegetation structure in managed forage production systems, either by alternately resting cool-season and warm-season grass forage fields or by leaving unharvested field borders, should provide refugia for small mammals during haying events.

Diversified cropping systems support greater microbial cycling and retention of carbon and nitrogen

Energy Technology Data Exchange (ETDEWEB)

King, Alison E.; Hofmockel, Kirsten S.

2017-03-01

Diversifying biologically simple cropping systems often entails altering other management practices, such as tillage regime or nitrogen (N) source. We hypothesized that the interaction of crop rotation, N source, and tillage in diversified cropping systems would promote microbially-mediated soil C and N cycling while attenuating inorganic N pools. We studied a cropping systems trial in its 10th year in Iowa, USA, which tested a 2-yr cropping system of corn (Zea mays L.)/soybean [Glycine max (L.) Merr.] managed with conventional fertilizer N inputs and conservation tillage, a 3-yr cropping system of corn/soybean/small grain + red clover (Trifolium pratense L.), and a 4-yr cropping system of corn/soybean/small grain + alfalfa (Medicago sativa L.)/alfalfa. Three year and 4-yr cropping systems were managed with composted manure, reduced N fertilizer inputs, and periodic moldboard ploughing. We assayed soil microbial biomass carbon (MBC) and N (MBN), soil extractable NH4 and NO3, gross proteolytic activity of native soil, and potential activity of six hydrolytic enzymes eight times during the growing season. At the 0-20cm depth, native protease activity in the 4-yr cropping system was greater than in the 2-yr cropping system by a factor of 7.9, whereas dissolved inorganic N pools did not differ between cropping systems (P = 0.292). At the 0-20cm depth, MBC and MBN the 4-yr cropping system exceeded those in the 2-yr cropping system by factors of 1.51 and 1.57. Our findings suggest that diversified crop cropping systems, even when periodically moldboard ploughed, support higher levels of microbial biomass, greater production of bioavailable N from SOM, and a deeper microbially active layer than less diverse cropping systems.

Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment.

Science.gov (United States)

Lipsewers, Yvonne A; Vasquez-Cardenas, Diana; Seitaj, Dorina; Schauer, Regina; Hidalgo-Martinez, Silvia; Sinninghe Damsté, Jaap S; Meysman, Filip J R; Villanueva, Laura; Boschker, Henricus T S

2017-05-15

multidisciplinary investigation of the sediments in a seasonally hypoxic coastal basin confirms this hypothesis. Our data show that bacterial community structure and chemolithoautotrophic activity varied with the seasonal depletion of oxygen. Unexpectedly, the dark carbon fixation was also dependent on the dominant microbial pathway of sulfur oxidation occurring in the sediment (i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae ). These results suggest that a complex niche partitioning within the sulfur-oxidizing bacterial community additionally affects the chemolithoautotrophic community of seasonally hypoxic sediments. Copyright © 2017 American Society for Microbiology.

Hydrodynamics of microbial filter feeding

DEFF Research Database (Denmark)

Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia

2017-01-01

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate......-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude......; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet...

Winter survival of microbial contaminants in soil: an in situ verification.

Science.gov (United States)

Bucci, Antonio; Allocca, Vincenzo; Naclerio, Gino; Capobianco, Giovanni; Divino, Fabio; Fiorillo, Francesco; Celico, Fulvio

2015-01-01

The aim of the research was to evaluate, at site scale, the influence of freezing and freeze/thaw cycles on the survival of faecal coliforms and faecal enterococci in soil, in a climate change perspective. Before the winter period and during grazing, viable cells of faecal coliforms and faecal enterococci were detected only in the first 10 cm below ground, while, after the winter period and before the new seasonal grazing, a lower number of viable cells of both faecal indicators was detected only in some of the investigated soil profiles, and within the first 5 cm. Taking into consideration the results of specific investigations, we hypothesise that the non-uniform spatial distribution of grass roots within the studied soil can play an important role in influencing this phenomenon, while several abiotic factors do not play any significant role. Taking into account the local trend in the increase of air temperature, a different distribution of microbial pollution over time is expected in spring waters, in future climate scenarios. The progressive increase in air temperature will cause a progressive decrease in freeze/thaw cycles at higher altitudes, minimising cold shocks on microbial cells, and causing spring water pollution also during winter. Copyright © 2014. Published by Elsevier B.V.

Impact of a high severity wildfire and two post-fire stabilisation treatments on the structure of the microbial community in a soil located in Laza (Ourense, NW Spain

Directory of Open Access Journals (Sweden)

A. Lombao

2013-01-01

Full Text Available Studies concerning the microbial communities in burnt soils have been focused on biochemical properties and, despite its interest, information about the microbial community structure is scarce. The aim of this study was to evaluate the short- and medium- term effects produced by a high severity fire and the application of post-fire stabilization methods (mulching and seeding in the structure of soil microbial population, determined by means of the analysis of phospholipid fatty acids (PLFA. The study was performed in a forest ecosystem affected by a high severity wildfire and highly susceptible to post-fire soil erosion (Laza, NW Spain. Samples were collected from the A horizon (0-2 cm immediately and 4, 8 and 12 months after the wildfire. The results of principal component analysis carried out with PLFA data make possible to differentiate between burnt and unburnt samples, indicating a clear effect of the wildfire on composition of microbial communities. Unburnt samples were characterized by the presence of fungal fatty acid as 18:2ω6, 18:1ω9 o 16:ω5, whereas fatty acid characteristics of actinomycetes tended to be higher in burnt samples than in the corresponding unburnt samples. The structure of microbial communities also varied with sampling time, confirming seasonal fluctuations of soil microbial parameters.

Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

Science.gov (United States)

Hyde, A.; Joye, S. B.; Teske, A.

2017-12-01

Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

Microbial electrode sensor for alcohols

Energy Technology Data Exchange (ETDEWEB)

Hikuma, M [Ajinomoto Co., Inc., Kawasaki, Japan; Kubo, T; Yasuda, T; Karube, I; Suzuki, S

1979-10-01

A microbial electrode consisting of immobilized microorganisms, a gas permeable Teflon membrane, and an oxygen electrode was prepared for the continuous determination of methyl and ethyl alcohols. Immobilized Trichosporon brassicae was employed for a microbial electrode sensor for ethyl alcohol. When a sample solution containing ethyl alcohol was injected into a microbial electrode system, the current of the electrode decreased markedly with time until a steady state was reached. The response time was within 10 min by the steady state method and within 6 min by the pulse method. A linear relationship was observed between the current decrease and the concentration of ethyl alcohol below 22.5 mg/liter. The current was reproducible within +- 6% of the relative error when a sample solution containing 16.5 mg/liter ethyl alcohol. The standard deviation was 0.5 mg/liter in 40 experiments. The selectivity of the microbial electrode sensor for ethyl alcohol was satisfactory. The microbial electrode sensor was applied to a fermentation broth of yeasts and satisfactory comparative results were obtained (correlation coefficient 0.98). The current output of the microbial electrode sensor was almost constant for more than three weeks and 2100 assays. A microbial electrode sensor using immobilized bacteria for methyl alcohol was also described.

Global microbialization of coral reefs.

Science.gov (United States)

Haas, Andreas F; Fairoz, Mohamed F M; Kelly, Linda W; Nelson, Craig E; Dinsdale, Elizabeth A; Edwards, Robert A; Giles, Steve; Hatay, Mark; Hisakawa, Nao; Knowles, Ben; Lim, Yan Wei; Maughan, Heather; Pantos, Olga; Roach, Ty N F; Sanchez, Savannah E; Silveira, Cynthia B; Sandin, Stuart; Smith, Jennifer E; Rohwer, Forest

2016-04-25

Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.

Modeling seasonal water balance based on catchments' hedging strategy on evapotranspiration for climate seasonality

Science.gov (United States)

Wu, S.; Zhao, J.; Wang, H.

2017-12-01

This paper develops a seasonal water balance model based on the hypothesis that natural catchments utilize hedging strategy on evapotranspiration for climate seasonality. According to the monthly aridity index, one year is split into wet season and dry season. A seasonal water balance model is developed by analogy to a two-stage reservoir operation model, in which seasonal rainfall infiltration, evapotranspiration and saturation-excess runoff is corresponding to the inflow, release and surplus of the catchment system. Then the optimal hedging between wet season and dry season evapotranspiration is analytically derived with marginal benefit principle. Water budget data sets of 320 catchments in the United States covering the period from 1980 to 2010 are used to evaluate the performance of this model. The Nash-Sutcliffe Efficiency coefficient for evapotranspiration is higher than 0.5 in 84% of the study catchments; while the runoff is 87%. This paper validates catchments' hedging strategy on evapotranspiration for climate seasonality and shows its potential application for seasonal water balance, which is valuable for water resources planning and management.

Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils

Directory of Open Access Journals (Sweden)

Daniel Renato Lammel

2015-10-01

Full Text Available Ecological processes regulating soil carbon (C and nitrogen (N cycles are still poorly understood, especially in the world’s largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA. Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA and Archaea, however forest soils showed the highest abundances of denitrifiers (nirK, nosZ and high N, which correlated with increased N2O emissions. Methanogens (mcrA and methanotrophs (pmoA were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches

Linking microbial diversity and functionality of arctic glacial surface habitats.

Science.gov (United States)

Lutz, Stefanie; Anesio, Alexandre M; Edwards, Arwyn; Benning, Liane G

2017-02-01

Distinct microbial habitats on glacial surfaces are dominated by snow and ice algae, which are the critical players and the dominant primary colonisers and net producers during the melt season. Here for the first time we have evaluated the role of these algae in association with the full microbial community composition (i.e., algae, bacteria, archaea) in distinct surface habitats and on 12 glaciers and permanent snow fields in Svalbard and Arctic Sweden. We cross-correlated these data with the analyses of specific metabolites such as fatty acids and pigments, and a full suite of potential critical physico-chemical parameters including major and minor nutrients, and trace metals. It has been shown that correlations between single algal species, metabolites, and specific geochemical parameters can be used to unravel mixed metabolic signals in complex communities, further assign them to single species and infer their functionality. The data also clearly show that the production of metabolites in snow and ice algae is driven mainly by nitrogen and less so by phosphorus limitation. This is especially important for the synthesis of secondary carotenoids, which cause a darkening of glacial surfaces leading to a decrease in surface albedo and eventually higher melting rates. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

KAUST Repository

Bayer, Kristina

2015-01-08

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

KAUST Repository

Bayer, Kristina; Moitinho-Silva, Lucas; Brü mmer, Franz; Cannistraci, Carlo V.; Ravasi, Timothy; Hentschel, Ute

2015-01-01

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

Emergence of serine carbapenemases (KPC and SME) among clinical strains of Enterobacteriaceae isolated in the United States Medical Centers: report from the MYSTIC Program (1999-2005).

Science.gov (United States)

Deshpande, Lalitagauri M; Rhomberg, Paul R; Sader, Helio S; Jones, Ronald N

2006-12-01

Among 8885 Enterobacteriaceae tested in the 1999 to 2005 period as part of the USA Meropenem Yearly Susceptibility Test Information Collection (MYSTIC) Program, 51 strains with increased imipenem and meropenem MIC values (> or =2 microg/mL) were detected. bla(KPC) was identified from 28 Klebsiella pneumoniae from 3 medical centers in the New York City area (8 ribotypes), 2 Klebsiella oxytoca from Arkansas (same ribotype), 7 Citrobacter freundii (6 from New York [5 ribotypes] and 1 from Delaware), 4 Enterobacter spp. from New York (2 species, different ribotypes), 3 Escherichia coli (2 from New York and 1 from Ohio, same ribotype), and 1 Serratia marcescens (New York). Sequencing confirmed KPC-2 or -3 in all of the strains. S. marcescens strains harboring SME-1 (2 isolates, same ribotype) and SME-2 (1 isolate) were identified from medical centers in Illinois and Washington state, respectively. Our results indicate that bla(KPC-2/3) has emerged widely (New York City area, Arkansas, Delaware, and Ohio) among Enterobacteriaceae isolated in the MYSTIC Program participant sites (2000-2005) and continues to be isolated from multiple species, as a result of clonal expansion and horizontal gene transfer. The escalating occurrence (0.35%) of serine carbapenemases could compromise the role of carbapenems and other beta-lactams in USA clinical practice although observed in only a few locations to date.

New microbial resource: microbial diversity, function and dynamics in Chinese liquor starter.

Science.gov (United States)

Huang, Yuhong; Yi, Zhuolin; Jin, Yanling; Zhao, Yonggui; He, Kaize; Liu, Dayu; Zhao, Dong; He, Hui; Luo, Huibo; Zhang, Wenxue; Fang, Yang; Zhao, Hai

2017-11-06

Traditional Chinese liquor (Baijiu) solid state fermentation technology has lasted for several thousand years. The microbial communities that enrich in liquor starter are important for fermentation. However, the microbial communities are still under-characterized. In this study, 454 pyrosequencing technology was applied to comprehensively analyze the microbial diversity, function and dynamics of two most-consumed liquor starters (Jiang- and Nong-flavor) during production. In total, 315 and 83 bacterial genera and 72 and 47 fungal genera were identified in Jiang- and Nong-flavor liquor starter, respectively. The relatively high diversity was observed when the temperature increased to 70 and 62 °C for Jiang- and Nong-flavor liquor starter, respectively. Some thermophilic fungi have already been isolated. Microbial communities that might contribute to ethanol fermentation, saccharification and flavor development were identified and shown to be core communities in correlation-based network analysis. The predictively functional profile of bacterial communities showed significant difference in energy, carbohydrate and amino acid metabolism and the degradation of aromatic compounds between the two kinds of liquor starters. Here we report these liquor starters as a new functionally microbial resource, which can be used for discovering thermophilic and aerobic enzymes and for food and feed preservation.

Enteric Infections Circulating during Hajj Seasons, 2011–2013

KAUST Repository

Abd El Ghany, Moataz; Alsomali, Mona; Almasri, Malak; Padron Regalado, Eriko; Naeem, Raeece; Tukestani, AbdulHafeez; Asiri, Abdullah; Hill-Cawthorne, Grant A.; Pain, Arnab; Memish, Ziad A.

2017-01-01

Hajj, the annual Muslim pilgrimage to Mecca, Saudi Arabia, is a unique mass gathering event that raises public health concerns in the host country and globally. Although gastroenteritis and diarrhea are common among Hajj pilgrims, the microbial etiologies of these infections are unknown. We collected 544 fecal samples from pilgrims with medically attended diarrheal illness from 40 countries during the 2011-2013 Hajj seasons and screened the samples for 16 pathogens commonly associated with diarrheal infections. Bacteria were the main agents detected, in 82.9% of the 228 positive samples, followed by viral (6.1%) and parasitic (5.3%) agents. Salmonella spp., Shigella/enteroinvasive Escherichia coli, and enterotoxigenic E. coli were the main pathogens associated with severe symptoms. We identified genes associated with resistance to third-generation cephalosporins approximate to 40% of Salmonella- and E. coli-positive samples. Hajj-associated foodborne infections pose a major public health risk through the emergence and transmission of antimicrobial drug-resistant bacteria.

Enteric Infections Circulating during Hajj Seasons, 2011–2013

KAUST Repository

Abd El Ghany, Moataz

2017-09-13

Hajj, the annual Muslim pilgrimage to Mecca, Saudi Arabia, is a unique mass gathering event that raises public health concerns in the host country and globally. Although gastroenteritis and diarrhea are common among Hajj pilgrims, the microbial etiologies of these infections are unknown. We collected 544 fecal samples from pilgrims with medically attended diarrheal illness from 40 countries during the 2011-2013 Hajj seasons and screened the samples for 16 pathogens commonly associated with diarrheal infections. Bacteria were the main agents detected, in 82.9% of the 228 positive samples, followed by viral (6.1%) and parasitic (5.3%) agents. Salmonella spp., Shigella/enteroinvasive Escherichia coli, and enterotoxigenic E. coli were the main pathogens associated with severe symptoms. We identified genes associated with resistance to third-generation cephalosporins approximate to 40% of Salmonella- and E. coli-positive samples. Hajj-associated foodborne infections pose a major public health risk through the emergence and transmission of antimicrobial drug-resistant bacteria.

Deep subsurface microbial processes

Science.gov (United States)

Lovley, D.R.; Chapelle, F.H.

1995-01-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

The maturing of microbial ecology.

Science.gov (United States)

Schmidt, Thomas M

2006-09-01

A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.

In-Drift Microbial Communities

Energy Technology Data Exchange (ETDEWEB)

D. Jolley

2000-11-09

As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

In-Drift Microbial Communities

International Nuclear Information System (INIS)

Jolley, D.

2000-01-01

As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses

Generation of Electricity and Analysis of Microbial Communities in Wheat Straw Biomass-Powered Microbial Fuel Cells

DEFF Research Database (Denmark)

Zhang, Yifeng; Min, Booki; Huang, L.

2009-01-01

Electricity generation from wheat straw hydrolysate and the microbial ecology of electricity producing microbial communities developed in two chamber microbial fuel cells (MFCs) were investigated. Power density reached 123 mW/m2 with an initial hydrolysate concentration of 1000 mg-COD/L while...

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell.

Science.gov (United States)

Timmers, Ruud A; Rothballer, Michael; Strik, David P B T B; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

2012-04-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors.

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

Energy Technology Data Exchange (ETDEWEB)

Timmers, Ruud A.; Strik, David P.B.T.B.; Hamelers, Bert; Buisman, Cees [Wageningen Univ. (Netherlands). Sub-dept. of Environmental Technology; Rothballer, Michael; Hartmann, Anton [Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg (Germany). Dept. Microbe-Plant Interactions; Engel, Marion; Schulz, Stephan; Schloter, Michael [Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg (Germany). Dept. Terrestrial Ecogenetics

2012-04-15

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors. (orig.)

Seasonality, mobility, and livability.

Science.gov (United States)

2012-01-31

Signature project 4a, Seasonality, Mobility, and Livability investigated the effects of weather, season, built environment, community amenities, attitudes, and demographics on mobility and quality of life (QOL). A four season panel survey exami...

Toward Understanding, Managing, and Protecting Microbial Ecosystems

Science.gov (United States)

Bodelier, Paul L. E.

2011-01-01

Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity–conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology. PMID:21747797

Towards understanding, managing and protecting microbial ecosystems

Directory of Open Access Journals (Sweden)

Paul eBodelier

2011-04-01

Full Text Available Microbial communities are at the very basis of life on earth, catalysing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper indentifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.

Toward understanding, managing, and protecting microbial ecosystems.

Science.gov (United States)

Bodelier, Paul L E

2011-01-01

Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity-conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.

Microbial accumulation of uranium

International Nuclear Information System (INIS)

Zhang Wei; Dong Faqin; Dai Qunwei

2005-01-01

The mechanism of microbial accumulation of uranium and the effects of some factors (including pH, initial uranium concentration, pretreatment of bacteria, and so on) on microbial accumulation of uranium are discussed briefly. The research direction and application prospect are presented. (authors)

Seasonal Allergies (Hay Fever)

Science.gov (United States)

... Safe Videos for Educators Search English Español Seasonal Allergies (Hay Fever) KidsHealth / For Parents / Seasonal Allergies (Hay ... español Alergia estacional (fiebre del heno) About Seasonal Allergies "Achoo!" It's your son's third sneezing fit of ...

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station

Science.gov (United States)

Repert, Deborah A.; Underwood, Jennifer C.; Smith, Richard L.; Song, Bongkeun

2014-01-01

Information on the contribution of nitrogen (N)-cycling processes in bed sediments to river nutrient fluxes in large northern latitude river systems is limited. This study examined the relationship between N-cycling processes in bed sediments and N speciation and loading in the Yukon River near its mouth at the Bering Sea. We conducted laboratory bioassays to measure N-cycling processes in sediment samples collected over distinct water cycle seasons. In conjunction, the microbial community composition in the bed sediments using genes involved in N-cycling (narG, napA, nosZ, and amoA) and 16S rRNA gene pyrosequences was examined. Temporal variation was observed in net N mineralization, nitrate uptake, and denitrification rate potentials and correlated strongly with sediment carbon (C) and extractable N content and microbial community composition rather than with river water nutrient concentrations. The C content of the bed sediment was notably impacted by the spring flood, ranging from 1.1% in the midst of an ice-jam to 0.1% immediately after ice-out, suggesting a buildup of organic material (OM) prior to scouring of the bed sediments during ice break up. The dominant members of the microbial community that explained differences in N-processing rates belonged to the genera Crenothrix,Flavobacterium, and the family of Comamonadaceae. Our results suggest that biogeochemical processing rates in the bed sediments appear to be more coupled to hydrology, nutrient availability in the sediments, and microbial community composition rather than river nutrient concentrations at Pilot Station.

Shifts in the microbial community structure explain the response of soil respiration to land-use change but not to climate warming

DEFF Research Database (Denmark)

Nazaries, Loïc; Tottey, William; Robinson, Lucinda

2015-01-01

Soil stores more carbon (C) than plants and atmosphere combined and it is vulnerable to increased microbial respiration under projected global changes including land-use change and future climate scenarios (mainly elevated temperature). Land-use change is known to have a direct impact on soil...... of this feedback response of Rs to global change. To identify the mechanisms of Rs response to land-use change and climate warming, we first investigated Rs from different land use types. Soil respiration was estimated seasonally from four different Scottish land uses: moorland, birch woodland, grassland and pine......, estimated by Multiplex Terminal-Restriction Fragment Length Polymorphism (MT-RFLP) and 454 pyrosequencing, was significantly different under each land use type. A strong correlation of Rs with soil properties (pH, inorganic N, C:N ratio and moisture) and with microbial community structure was identified...

Seasonal reproduction of vampire bats and its relation to seasonality of bovine rabies.

Science.gov (United States)

Lord, R D

1992-04-01

Studies of pregnancy and lactation in vampire bats (Desmodus rotundus) in northern Argentina over a 4 yr period showed an inverse relationship between prevalence of pregnancy and lactation, the consequence of birth and onset of lactation, which was correlated with the wet season. The seasonal influx of young susceptibles into the vampire population in the wet season coincided with the well known increase in vampire transmitted rabies in that season.

Microbial risk in wastewater irrigated lettuce: comparing Escherichia coli contamination from an experimental site with a laboratory approach.

Science.gov (United States)

Makkaew, P; Miller, M; Fallowfield, H J; Cromar, N J

This study assessed the contamination of Escherichia coli, in lettuce grown with treated domestic wastewater in four different irrigation configurations: open spray, spray under plastic sheet cover, open drip and drip under plastic sheet cover. Samples of lettuce from each irrigation configuration and irrigating wastewater were collected during the growing season. No E. coli was detected in lettuce from drip irrigated beds. All lettuce samples from spray beds were positive for E. coli, however, no statistical difference (p > 0.05) was detected between lettuces grown in open spray or covered spray beds. The results from the field experiment were also compared to a laboratory experiment which used submersion of lettuce in wastewater of known E. coli concentration as a surrogate method to assess contamination following irrigation. The microbial quality of spray bed lettuces was not significantly different from submersed lettuce when irrigated with wastewater containing 1,299.7 E. coli MPN/100 mL (p > 0.05). This study is significant since it is the first to validate that the microbial contamination of lettuce irrigated with wastewater in the field is comparable with a laboratory technique frequently applied in the quantitative microbial risk assessment of the consumption of wastewater irrigated salad crops.

Monitoring of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis.

Science.gov (United States)

Tanaka, Yasushi; Watanabe, Jun; Mogi, Yoshinobu

2012-08-01

Soy sauce is a traditional seasoning produced through the fermentation of soybeans and wheat using microbes. In this study, the microbial communities involved in the soy sauce manufacturing process were analyzed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The bacterial DGGE profile indicated that the bacterial microbes in the koji were Weissella cibaria (Weissella confusa, Weissella kimchii, Weissella salipiscis, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus iners, or Streptococcus thermophilus), Staphylococcus gallinarum (or Staphylococcus xylosus), and Staphylococcus kloosii. In addition to these bacteria, Tetragenococcus halophilus was also detected in the mash during lactic acid fermentation. The fungal DGGE profile indicated that the fungal microbes in the koji were not only Aspergillus oryzae but also several yeasts. In the mash, Zygosaccharomyces rouxii appeared in the early fermentation stage, Candida etchellsii (or Candida nodaensis) and Candida versatilis were detected at the middle fermentation stage, and Candida etchellsii was detected at the mature fermentation stage. These results suggest that the microbial communities present during the soy sauce manufacturing process change drastically throughout its production. This is the first report to reveal the microbial communities involved in the soy sauce manufacturing process using a culture-independent method. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

Application of biocathode in microbial fuel cells: cell performance and microbial community

Energy Technology Data Exchange (ETDEWEB)

Guo-Wei, Chen [Pusan National Univ. (Korea). Dept. of Environmental Engineering; Hefei Univ. of Technology (China). School of Civil Engineering; Choi, Soo-Jung; Lee, Tae-Ho; Lee, Gil-Young; Cha, Jae-Hwan; Kim, Chang-Won [Pusan National Univ. (Korea). Dept. of Environmental Engineering

2008-06-15

Instead of the utilization of artificial redox mediators or other catalysts, a biocathode has been applied in a two-chamber microbial fuel cell in this study, and the cell performance and microbial community were analyzed. After a 2-month startup, the microorganisms of each compartment in microbial fuel cell were well developed, and the output of microbial fuel cell increased and became stable gradually, in terms of electricity generation. At 20 ml/min flow rate of the cathodic influent, the maximum power density reached 19.53 W/m{sup 3}, while the corresponding current and cell voltage were 15.36 mA and 223 mV at an external resistor of 14.9 {omega}, respectively. With the development of microorganisms in both compartments, the internal resistance decreased from initial 40.2 to 14.0 {omega}, too. Microbial community analysis demonstrated that five major groups of the clones were categorized among those 26 clone types derived from the cathode microorganisms. Betaproteobacteria was the most abundant division with 50.0% (37 of 74) of the sequenced clones in the cathode compartment, followed by 21.6% (16 of 74) Bacteroidetes, 9.5% (7 of 74) Alphaproteobacteria, 8.1% (6 of 74) Chlorobi, 4.1% (3 of 74) Deltaproteobacteria, 4.1% (3 of 74) Actinobacteria, and 2.6% (2 of 74) Gammaproteobacteria. (orig.)

B-Vitamin Competition: Intracellular and Dissolved B-Vitamins Provide Insight into Marine Microbial Community Dynamics

Science.gov (United States)

Suffridge, C.; Gomez-Consarnau, L.; Qu, P.; Tenenbaum, N.; Fu, F.; Hutchins, D. A.; Sanudo-Wilhelmy, S. A.

2016-02-01

The availability of B-vitamins has the ability to directly affect the dynamics of the marine microbial community. Here we show, for the first time, the connection between dissolved and intracellular B-vitamins in a marine environmental community. Two incubation experiments were conducted at a long-term study site (SPOT) in the San Pedro Basin off the coast of Los Angeles, CA. Experiments were conducted in oligotrophic, preupwelling conditions. Due to the 2015 El Niño event, the seasonal upwelling at SPOT did not occur, creating unusually nutrient depleted conditions. Vitamins B1, B7, and B12 were added in addition to macronutrients at concentrations similar to typical SPOT upwelling conditions. Intracellular and dissolved B-vitamin analyses were conducted to determine shifts in cellular B-vitamin requirements as a function of growth rate. We observed a significant bacterioplankton and phytoplankton growth responses with the addition of B-vitamins in a manner that appears to match the enzymatic requirements for these compounds (e.g. B1>B7>B12). Intracellular B-vitamin analysis of T0 samples support this observation, as all four forms of B12 were not detectable within cells, yet multiple forms of B1 and B7 were detected at or near levels previously reported. Treatments with B12 and macronutrients were observed to have the greatest growth rates. This finding, in addition to the apparent lack of intracellular B12 in the initial community, appears to indicate that the initial microbial community was limited by B12. The addition of each vitamin caused a distinct shift in the blooming microbial community. Our results demonstrate that B-vitamins strongly influence not only the growth rate, but also the species composition and species succession of the microbial community as a whole. Large-scale changes to upwelling regimes are predicted in the future ocean; our results indicate that B-vitamins will have a substantial role in controlling microbial community dynamics under

Microbial populations in an agronomically managed mollisol treated with simulated acid rain

International Nuclear Information System (INIS)

Miller, K.W.; Cole, M.A.; Banwart, W.L.

1991-01-01

A fertile well-buffered mollisol (Flanagan silt loam, fine montmorillonitic mesic Aquic Arguidoll) under cultivation with corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] was subjected to simulated rain of pH 5.6, 4.2, and 3.0, while moisture-activated rain exclusion shelters provided protection from ambient rain. Soil was sampled to a depth of 3 cm on four dates throughout the 1985 growing season. The following microorganisms were enumerated by plate counts or most probable number: general heterotrophic bacteria, general soil fungi, free-living N-fixing bacteria, fluorescent pseudomonads, autotrophic ammonium-oxidizing, nitrite-oxidizing, and thio-sulfate-oxidizing bacteria. The ANOVA was used to determine the combined and individual effects of rain treatments, crop field, and sampling date. Crop field and sampling date affected microbial numbers more than rain treatments. Overall, rain treatment effects were limited to nitrite-oxidizing bacteria; lower numbers occurred in the corn field in subplots treated with rain of pH 4.2 and 3.0, and in the soybean field treated with rain of pH 3.0. The trend was strongest in June and July. In the corn field in subplots treated with rain of pH 3.0, numbers of thiosulfate-oxidizing bacteria were higher an numbers of general heterotrophic bacteria were lower; however, these trends were comparatively weak. Rain treatments caused essentially no decrease in soil pH, suggesting that acid rain constituents affect certain microbial populations without causing overt changes in pH. Because they appear to be unusually sensitive, nitrite-oxidizing bacteria could be used as experimental indicators of changes in soil microbial communities subjected to acid rain

Microbial production of gaseous hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Fukuda, Hideo

1987-10-20

Microbial production of ethylene, isobutane and a saturated gaseous hydrocarbon mixture was described. Microbial ethylene production was studied with Penicillium digitatum IFO 9372 and a novel pathway of the ethylene biosynthesis through alpha-ketoglutarate was proposed. Rhodotorula minuta IFO 1102 was selected for the microbial production of isobutane and the interesting actions of L-leucine and L-phenylalanine for the isobutane production were found. It was finally presented about the microbial production of a saturated gaseous hydrocarbon mixture with Rhizopus japonicus IFO 4758 was described. A gas mixture was produced through a chemical reaction of SH compounds and some cellular component such as squalene under aerobic conditions. (4 figs, 7 tabs, 41 refs)

Microbial control of pollution

Energy Technology Data Exchange (ETDEWEB)

Fry, J C; Gadd, G M; Herbert, R A; Jones, C W; Watson-Craik, I A [eds.

1992-01-01

12 papers are presented on the microbial control of pollution. Topics covered include: bioremediation of oil spills; microbial control of heavy metal pollution; pollution control using microorganisms and magnetic separation; degradation of cyanide and nitriles; nitrogen removal from water and waste; and land reclamation and restoration.

Soil microbial responses to climate warming in Northern Andean alpine ecosystems

Science.gov (United States)

Gallery, R. E.; Lasso, E.

2017-12-01

The historically cooler temperatures and waterlogged soils of tropical alpine grasslands (páramo) have resulted in low decomposition rates and a large buildup of organic matter, making páramo one of the most important carbon sinks in tropical biomes. The climatic factors that favored the carbon accumulation are changing, and as a result páramo could play a disproportionate role in driving climate feedbacks through increased carbon released from these large soil carbon stores. Open top chamber warming experiments were established in the Colombian Andes in 2016 to quantify the magnitude of climate change on carbon balance and identify microbial and plant traits that regulate these impacts. Two focal sites differ in mean annual temperature, precipitation, and plant community richness. Heterotrophic respiration (RH,) was measured from soil cores incubated at temperatures representing current and projected warming. The warming effect on RH was sensitive to soil moisture, which could reflect shifts in microbial community composition and/or extracellular enzyme production or efficiency as soils dry. Bacterial, archaeal, and fungal communities in ambient and warmed plots were measured through high-throughput amplicon sequencing of the 16S rRNA and ITS1 rRNA gene regions. Communities showed strong spatial structuring both within and among páramo, reflecting the topographic heterogeneity of these ecosystems. Significant differences in relative abundance of dominant microbial taxa between páramo could be largely explained by soil bulk density, water holding capacity, and non-vascular plant cover. Phototrophs common to anoxic soils (e.g., Rhodospirillaceae, Hyphomicrobiaceae) were abundant. Taxa within Euryarchaeota were recovered, suggesting methanogenesis potential. Exploration of the magnitude and temperature sensitivity of methane flux is needed in these seasonally anoxic soils whose dynamics could have significant implications for the global climate system.

Copper removal and microbial community analysis in single-chamber microbial fuel cell.

Science.gov (United States)

Wu, Yining; Zhao, Xin; Jin, Min; Li, Yan; Li, Shuai; Kong, Fanying; Nan, Jun; Wang, Aijie

2018-04-01

In this study, copper removal and electricity generation were investigated in a single-chamber microbial fuel cell (MFC). Result showed that copper was efficiently removed in the membrane-less MFC with removal efficiency of 98.3% at the tolerable Cu 2+ concentration of 12.5 mg L -1 , the corresponding open circuit voltage and maximum power density were 0.78 V and 10.2 W m -3 , respectively. The mechanism analysis demonstrated that microbial electrochemical reduction contributed to the copper removal with the products of Cu and Cu 2 O deposited at biocathode. Moreover, the microbial community analysis indicated that microbial communities changed with different copper concentrations. The dominant phyla were Proteobacteria and Bacteroidetes which could play key roles in electricity generation, while Actinobacteria and Acidobacteria were also observed which were responsible for Cu-resistant and copper removal. It will be of important guiding significance for the recovery of copper from low concentration wastewater through single-chamber MFC with simultaneous energy recovery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell

Science.gov (United States)

Miceli, Joseph F.; Garcia-Peña, Ines; Parameswaran, Prathap; Torres, César I.; Krajmalnik-Brown, Rosa

2014-01-01

Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (~11 A/m2) and Coulombic efficiency (~70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ~80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed micro bial cultures containing complementing biochemical pathways. PMID:25048958

Towards the understanding of microbial metabolism in relation to microbial enhanced oil recovery

DEFF Research Database (Denmark)

Halim, Amalia Yunita; Nielsen, Sidsel Marie; Nielsen, Kristian Fog

2017-01-01

In this study, Bacillus licheniformis 421 was used as a model organism to understand the effects of microbial cell growth and metabolite production under anaerobic conditions in relation to microbial enhanced oil recovery. The bacterium was able to grow anaerobically on different carbon compounds...

GloFAS-Seasonal: Operational Seasonal Ensemble River Flow Forecasts at the Global Scale

Science.gov (United States)

Emerton, Rebecca; Zsoter, Ervin; Smith, Paul; Salamon, Peter

2017-04-01

Seasonal hydrological forecasting has potential benefits for many sectors, including agriculture, water resources management and humanitarian aid. At present, no global scale seasonal hydrological forecasting system exists operationally; although smaller scale systems have begun to emerge around the globe over the past decade, a system providing consistent global scale seasonal forecasts would be of great benefit in regions where no other forecasting system exists, and to organisations operating at the global scale, such as disaster relief. We present here a new operational global ensemble seasonal hydrological forecast, currently under development at ECMWF as part of the Global Flood Awareness System (GloFAS). The proposed system, which builds upon the current version of GloFAS, takes the long-range forecasts from the ECMWF System4 ensemble seasonal forecast system (which incorporates the HTESSEL land surface scheme) and uses this runoff as input to the Lisflood routing model, producing a seasonal river flow forecast out to 4 months lead time, for the global river network. The seasonal forecasts will be evaluated using the global river discharge reanalysis, and observations where available, to determine the potential value of the forecasts across the globe. The seasonal forecasts will be presented as a new layer in the GloFAS interface, which will provide a global map of river catchments, indicating whether the catchment-averaged discharge forecast is showing abnormally high or low flows during the 4-month lead time. Each catchment will display the corresponding forecast as an ensemble hydrograph of the weekly-averaged discharge forecast out to 4 months, with percentile thresholds shown for comparison with the discharge climatology. The forecast visualisation is based on a combination of the current medium-range GloFAS forecasts and the operational EFAS (European Flood Awareness System) seasonal outlook, and aims to effectively communicate the nature of a seasonal

Microbial respiration per unit microbial biomass increases with carbon-to-nutrient ratios in soils

Science.gov (United States)

Spohn, Marie; Chodak, Marcin

2015-04-01

The ratio of carbon-to-nutrient in forest floors is usually much higher than the ratio of carbon-to-nutrient that soil microorganisms require for their nutrition. In order to understand how this mismatch affects carbon cycling, the respiration rate per unit soil microbial biomass carbon - the metabolic quotient (qCO2) - was studied. This was done in a field study (Spohn and Chodak, 2015) and in a meta-analysis of published data (Spohn, 2014). Cores of beech, spruce, and mixed spruce-beech forest soils were cut into slices of 1 cm from the top of the litter layer down to 5 cm in the mineral soil, and the relationship between the qCO2 and the soil carbon-to-nitrogen (C:N) and the soil carbon-to-phosphorus (C:P) ratio was analyzed. We found that the qCO2 was positively correlated with soil C:N ratio in spruce soils (R = 0.72), and with the soil C:P ratio in beech (R = 0.93), spruce (R = 0.80) and mixed forest soils (R = 0.96). We also observed a close correlation between the qCO2 and the soil C concentration in all three forest types. Yet, the qCO2 decreased less with depth than the C concentration in all three forest types, suggesting that the change in qCO2 is not only controlled by the soil C concentration. We conclude that microorganisms increase their respiration rate per unit biomass with increasing soil C:P ratio and C concentration, which adjusts the substrate to their nutritional demands in terms of stoichiometry. In an analysis of literature data, I tested the effect of the C:N ratio of soil litter layers on microbial respiration in absolute terms and per unit microbial biomass C. For this purpose, a global dataset on the microbial respiration rate per unit microbial biomass C - termed the metabolic quotient (qCO2) - was compiled form literature data. It was found that the qCO2 in the soil litter layers was positively correlated with the litter C:N ratio and negatively related with the litter nitrogen (N) concentration. The positive relation between the qCO2

A Microbial Assessment Scheme to measure microbial performance of Food Safety Management Systems.

Science.gov (United States)

Jacxsens, L; Kussaga, J; Luning, P A; Van der Spiegel, M; Devlieghere, F; Uyttendaele, M

2009-08-31

A Food Safety Management System (FSMS) implemented in a food processing industry is based on Good Hygienic Practices (GHP), Hazard Analysis Critical Control Point (HACCP) principles and should address both food safety control and assurance activities in order to guarantee food safety. One of the most emerging challenges is to assess the performance of a present FSMS. The objective of this work is to explain the development of a Microbial Assessment Scheme (MAS) as a tool for a systematic analysis of microbial counts in order to assess the current microbial performance of an implemented FSMS. It is assumed that low numbers of microorganisms and small variations in microbial counts indicate an effective FSMS. The MAS is a procedure that defines the identification of critical sampling locations, the selection of microbiological parameters, the assessment of sampling frequency, the selection of sampling method and method of analysis, and finally data processing and interpretation. Based on the MAS assessment, microbial safety level profiles can be derived, indicating which microorganisms and to what extent they contribute to food safety for a specific food processing company. The MAS concept is illustrated with a case study in the pork processing industry, where ready-to-eat meat products are produced (cured, cooked ham and cured, dried bacon).

Hydrodynamics of microbial filter feeding.

Science.gov (United States)

Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H; Kiørboe, Thomas; Andersen, Anders

2017-08-29

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis , and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling.

Timing of Seasonal Sales.

OpenAIRE

Courty, Pascal; Li, Hao

1999-01-01

We present a model of timing of seasonal sales where stores choose several designs at the beginning of the season without knowing wich one, if any, will be fashionable. Fashionable designs have a chance to fetch high prices in fashion markets while non-fashionable ones must be sold in a discount market. In the beginning of the season, stores charge high prices in the hope of capturing their fashion market. As the end of the season approaches with goods still on the shelves, stores adjust down...

Microbial community composition of a down-flow hanging sponge (DHS) reactor combined with an up-flow anaerobic sludge blanket (UASB) reactor for the treatment of municipal sewage.

Science.gov (United States)

Kubota, Kengo; Hayashi, Mikio; Matsunaga, Kengo; Iguchi, Akinori; Ohashi, Akiyoshi; Li, Yu-You; Yamaguchi, Takashi; Harada, Hideki

2014-01-01

The microbial community composition of a down-flow hanging sponge (DHS) reactor in an up-flow anaerobic sludge blanket (UASB)-DHS system used for the treatment of municipal sewage was investigated. The clone libraries showed marked differences in microbial community composition at different reactor heights and in different seasons. The dominant phylotypes residing in the upper part of the reactor were likely responsible for removing organic matters because a significant reduction in organic matter in the upper part was observed. Quantification of the amoA genes revealed that the proportions of ammonia oxidizing bacteria (AOB) varied along the vertical length of the reactor, with more AOB colonizing the middle and lower parts of the reactor than the top of the reactor. The findings indicated that sewage treatment was achieved by a separation of microbial habitats responsible for organic matter removal and nitrification in the DHS reactor. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

Science.gov (United States)

Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

2015-12-01

Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined

Discrimination of chicken seasonings and beef seasonings using electronic nose and sensory evaluation.

Science.gov (United States)

Tian, Huaixiang; Li, Fenghua; Qin, Lan; Yu, Haiyan; Ma, Xia

2014-11-01

This study examines the feasibility of electronic nose as a method to discriminate chicken and beef seasonings and to predict sensory attributes. Sensory evaluation showed that 8 chicken seasonings and 4 beef seasonings could be well discriminated and classified based on 8 sensory attributes. The sensory attributes including chicken/beef, gamey, garlic, spicy, onion, soy sauce, retention, and overall aroma intensity were generated by a trained evaluation panel. Principal component analysis (PCA), discriminant factor analysis (DFA), and cluster analysis (CA) combined with electronic nose were used to discriminate seasoning samples based on the difference of the sensor response signals of chicken and beef seasonings. The correlation between sensory attributes and electronic nose sensors signal was established using partial least squares regression (PLSR) method. The results showed that the seasoning samples were all correctly classified by the electronic nose combined with PCA, DFA, and CA. The electronic nose gave good prediction results for all the sensory attributes with correlation coefficient (r) higher than 0.8. The work indicated that electronic nose is an effective method for discriminating different seasonings and predicting sensory attributes. © 2014 Institute of Food Technologists®

EVA Suit Microbial Leakage Investigation

Data.gov (United States)

National Aeronautics and Space Administration — The objective of this project is to collect microbial samples from various EVA suits to determine how much microbial contamination is typically released during...

Passive warming effect on soil microbial community and humic substance degradation in maritime Antarctic region.

Science.gov (United States)

Kim, Dockyu; Park, Ha Ju; Kim, Jung Ho; Youn, Ui Joung; Yang, Yung Hun; Casanova-Katny, Angélica; Vargas, Cristina Muñoz; Venegas, Erick Zagal; Park, Hyun; Hong, Soon Gyu

2018-06-01

Although the maritime Antarctic has undergone rapid warming, the effects on indigenous soil-inhabiting microorganisms are not well known. Passive warming experiments using open-top chamber (OTC) have been performed on the Fildes Peninsula in the maritime Antarctic since 2008. When the soil temperature was measured at a depth of 2-5 cm during the 2013-2015 summer seasons, the mean temperature inside OTC (OTC-In) increased by approximately 0.8 °C compared with outside OTC (OTC-Out), while soil chemical and physical characteristics did not change. Soils (2015 summer) from OTC-In and OTC-Out were subjected to analysis for change in microbial community and degradation rate of humic substances (HS, the largest pool of recalcitrant organic carbon in soil). Archaeal and bacterial communities in OTC-In were minimally affected by warming compared with those in OTC-Out, with archaeal methanogenic Thermoplasmata slightly increased in abundance. The abundance of heterotrophic fungi Ascomycota was significantly altered in OTC-In. Total bacterial and fungal biomass in OTC-In increased by 20% compared to OTC-Out, indicating that this may be due to increased microbial degradation activity for soil organic matter (SOM) including HS, which would result in the release of more low-molecular-weight growth substrates from SOM. Despite the effects of warming on the microbial community over the 8-years-experiments warming did not induce any detectable change in content or structure of polymeric HS. These results suggest that increased temperature may have significant and direct effects on soil microbial communities inhabiting maritime Antarctic and that soil microbes would subsequently provide more available carbon sources for other indigenous microbes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genome-wide analysis of positively selected genes in seasonal and non-seasonal breeding species.

Directory of Open Access Journals (Sweden)

Yuhuan Meng

Full Text Available Some mammals breed throughout the year, while others breed only at certain times of year. These differences in reproductive behavior can be explained by evolution. We identified positively-selected genes in two sets of species with different degrees of relatedness including seasonal and non-seasonal breeding species, using branch-site models. After stringent filtering by sum of pairs scoring, we revealed that more genes underwent positive selection in seasonal compared with non-seasonal breeding species. Positively-selected genes were verified by cDNA mapping of the positive sites with the corresponding cDNA sequences. The design of the evolutionary analysis can effectively lower the false-positive rate and thus identify valid positive genes. Validated, positively-selected genes, including CGA, DNAH1, INVS, and CD151, were related to reproductive behaviors such as spermatogenesis and cell proliferation in non-seasonal breeding species. Genes in seasonal breeding species, including THRAP3, TH1L, and CMTM6, may be related to the evolution of sperm and the circadian rhythm system. Identification of these positively-selected genes might help to identify the molecular mechanisms underlying seasonal and non-seasonal reproductive behaviors.

Microbial community production, respiration, and structure of the microbial food web of an ecosystem in the northeastern Atlantic Ocean

Science.gov (United States)

Maixandeau, Anne; LefèVre, Dominique; Karayanni, Hera; Christaki, Urania; van Wambeke, France; Thyssen, Melilotus; Denis, Michel; FernáNdez, Camila I.; Uitz, Julia; Leblanc, Karine; QuéGuiner, Bernard

2005-07-01

Gross community production (GCP), dark community respiration (DCR), and the biomass of the different size classes of organisms in the microbial community were measured in the northeastern Atlantic basin as part of the Programme Océan Multidisciplinaire Méso Echelle (POMME) project. The field experiment was conducted during three seasons (winter, spring, and late summer-fall) in 2001. Samples were collected from four different mesoscale structures within the upper 100 m. GCP rates increased from winter (101 ± 24 mmol O2 m-2 d-1) to spring (153 ± 27 mmol O2 m-2 d-1) and then decreased from spring to late summer (44 ± 18 mmol O2 m-2 d-1). DCR rates increased from winter (-47 ± 18 mmol O2 m-2 d-1) to spring (-97 ± 7 mmol O2 m-2 d-1) and then decreased from spring to late summer (50 ± 7 mmol O2 m-2 d-1). The onset of stratification depended on latitude as well as on the presence of mesoscale structures (eddies), and this largely contributed to the variability of GCP. The trophic status of the POMME area was defined as net autotrophic, with a mean annual net community production rate of +38 ± 18 mmol O2 m-2 d-1, exhibiting a seasonal variation from +2 ± 20 mmol O2 m-2 d-1 to +57 ± 20 mmol O2 m-2 d-1. This study highlights that small organisms (picoautotrophs, nanoautotrophs, and bacteria) are the main organisms contributing to biological fluxes throughout the year and that episodic blooms of microphytoplankton are related to mesoscale structures.

Seasonality and dietary requirements: will eating seasonal food contribute to health and environmental sustainability?

Science.gov (United States)

Macdiarmid, Jennie I

2014-08-01

Eating more seasonal food is one proposal for moving towards more sustainable consumption patterns, based on the assumption that it could reduce the environmental impact of the diet. The aim of the present paper is to consider the implications of eating seasonal food on the different elements of sustainability (i.e. health, economics, society), not just the environment. Seasonality can be defined as either globally seasonal (i.e. produced in the natural production season but consumed anywhere in the world) or locally seasonal (i.e. produced in the natural production season and consumed within the same climatic zone). The environmental, health, economic and societal impact varies by the definition used. Global seasonality has the nutritional benefit of providing a more varied and consistent supply of fresh produce year round, but this increases demand for foods that in turn can have a high environmental cost in the country of production (e.g. water stress, land use change with loss of biodiversity). Greenhouse gas emissions of globally seasonal food are not necessarily higher than food produced locally as it depends more on the production system used than transportation. Eating more seasonal food, however, is only one element of a sustainable diet and should not overshadow some of the potentially more difficult dietary behaviours to change that could have greater environmental and health benefits (e.g. reducing overconsumption or meat consumption). For future guidelines for sustainable diets to be realistic they will need to take into account modern lifestyles, cultural and social expectations in the current food environment.

MICROBIAL SURFACTANTS IN ENVIRONMENTAL TECHNOLOGIES

Directory of Open Access Journals (Sweden)

T. P. Pirog

2015-08-01

Full Text Available It was shown literature and own experimental data concerning the use of microbial surface active glycolipids (rhamno-, sophoro- and trehalose lipids and lipopeptides for water and soil purification from oil and other hydrocarbons, removing toxic heavy metals (Cu2+, Cd2+, Ni2+, Pb2+, degradation of complex pollution (oil and other hydrocarbons with heavy metals, and the role of microbial surfactants in phytoremediation processes. The factors that limit the use of microbial surfactants in environmental technologies are discussed. Thus, at certain concentrations biosurfactant can exhibit antimicrobial properties and inhibit microorganisms destructing xenobiotics. Microbial biodegradability of surfactants may also reduce the effectiveness of bioremediation. Development of effective technologies using microbial surfactants should include the following steps: monitoring of contaminated sites to determine the nature of pollution and analysis of the autochthonous microbiota; determining the mode of surfactant introduction (exogenous addition of stimulation of surfactant synthesis by autochthonous microbiota; establishing an optimal concentration of surfactant to prevent exhibition of antimicrobial properties and rapid biodegradation; research both in laboratory and field conditions.

Seasonal Variation in Epidemiology

Science.gov (United States)

Marrero, Osvaldo

2013-01-01

Seasonality analyses are important in medical research. If the incidence of a disease shows a seasonal pattern, then an environmental factor must be considered in its etiology. We discuss a method for the simultaneous analysis of seasonal variation in multiple groups. The nuts and bolts are explained using simple trigonometry, an elementary…

Seasonality of absolute humidity explains seasonality of influenza-like illness in Vietnam.

Science.gov (United States)

Thai, Pham Quang; Choisy, Marc; Duong, Tran Nhu; Thiem, Vu Dinh; Yen, Nguyen Thu; Hien, Nguyen Tran; Weiss, Daniel J; Boni, Maciej F; Horby, Peter

2015-12-01

Experimental and ecological studies have shown the role of climatic factors in driving the epidemiology of influenza. In particular, low absolute humidity (AH) has been shown to increase influenza virus transmissibility and has been identified to explain the onset of epidemics in temperate regions. Here, we aim to study the potential climatic drivers of influenza-like illness (ILI) epidemiology in Vietnam, a tropical country characterized by a high diversity of climates. We specifically focus on quantifying and explaining the seasonality of ILI. We used 18 years (1993-2010) of monthly ILI notifications aggregated by province (52) and monthly climatic variables (minimum, mean, maximum temperatures, absolute and relative humidities, rainfall and hours of sunshine) from 67 weather stations across Vietnam. Seasonalities were quantified from global wavelet spectra, using the value of the power at the period of 1 year as a measure of the intensity of seasonality. The 7 climatic time series were characterized by 534 summary statistics which were entered into a regression tree to identify factors associated with the seasonality of AH. Results were extrapolated to the global scale using simulated climatic times series from the NCEP/NCAR project. The intensity of ILI seasonality in Vietnam is best explained by the intensity of AH seasonality. We find that ILI seasonality is weak in provinces experiencing weak seasonal fluctuations in AH (annual power power >17.6). In Vietnam, AH and ILI are positively correlated. Our results identify a role for AH in driving the epidemiology of ILI in a tropical setting. However, in contrast to temperate regions, high rather than low AH is associated with increased ILI activity. Fluctuation in AH may be the climate factor that underlies and unifies the seasonality of ILI in both temperate and tropical regions. Alternatively, the mechanism of action of AH on disease transmission may be different in cold-dry versus hot-humid settings

Global Seasonality of Rotavirus Disease

Science.gov (United States)

Patel, Manish M.; Pitzer, Virginia; Alonso, Wladimir J.; Vera, David; Lopman, Ben; Tate, Jacqueline; Viboud, Cecile; Parashar, Umesh D.

2012-01-01

Background A substantial number of surveillance studies have documented rotavirus prevalence among children admitted for dehydrating diarrhea. We sought to establish global seasonal patterns of rotavirus disease before widespread vaccine introduction. Methods We reviewed studies of rotavirus detection in children with diarrhea published since 1995. We assessed potential relationships between seasonal prevalence and locality by plotting the average monthly proportion of diarrhea cases positive for rotavirus according to geography, country development, and latitude. We used linear regression to identify variables that were potentially associated with the seasonal intensity of rotavirus. Results Among a total of 99 studies representing all six geographical regions of the world, patterns of year-round disease were more evident in low- and low-middle income countries compared with upper-middle and high income countries where disease was more likely to be seasonal. The level of country development was a stronger predictor of strength of seasonality (P=0.001) than geographical location or climate. However, the observation of distinctly different seasonal patterns of rotavirus disease in some countries with similar geographical location, climate and level of development indicate that a single unifying explanation for variation in seasonality of rotavirus disease is unlikely. Conclusion While no unifying explanation emerged for varying rotavirus seasonality globally, the country income level was somewhat more predictive of the likelihood of having seasonal disease than other factors. Future evaluation of the effect of rotavirus vaccination on seasonal patterns of disease in different settings may help understand factors that drive the global seasonality of rotavirus disease. PMID:23190782

Nonbreeding-Season Drivers of Population Dynamics in Seasonal Migrants: Conservation Parallels Across Taxa

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Anna M. Calvert

2009-12-01

Full Text Available For seasonal migrants, logistical constraints have often limited conservation efforts to improving survival and reproduction during the breeding season only. Yet, mounting empirical evidence suggests that events occurring throughout the migratory life cycle can critically alter the demography of many migrant species. Herein, we build upon recent syntheses of avian migration research to review the role of non-breeding seasons in determining the population dynamics and fitness of diverse migratory taxa, including salmonid fishes, marine mammals, ungulates, sea turtles, butterflies, and numerous bird groups. We discuss several similarities across these varied migrants: (i non-breeding survivorship tends to be a strong driver of population growth; (ii non-breeding events can affect fitness in subsequent seasons through seasonal interactions at individual- and population-levels; (iii broad-scale climatic influences often alter non-breeding resources and migration timing, and may amplify population impacts through covariation among seasonal vital rates; and (iv changes to both stationary and migratory non-breeding habitats can have important consequences for abundance and population trends. Finally, we draw on these patterns to recommend that future conservation research for seasonal migrants will benefit from: (1 more explicit recognition of the important parallels among taxonomically diverse migratory animals; (2 an expanded research perspective focused on quantification of all seasonal vital rates and their interactions; and (3 the development of detailed population projection models that account for complexity and uncertainty in migrant population dynamics.

Microbial plankton communities in the coastal southeastern Black Sea: biomass, composition and trophic interactions

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Ulgen Aytan

2018-04-01

Full Text Available Summary: We investigated biomass and composition of the pico-, nano- and microplankton communities in a coastal station of the southeastern Black Sea during 2011. We also examined trophic interactions within these communities from size-fractionated dilution experiments in February, June and December. Autotrophic and heterotrophic biomasses showed similar seasonal trends, with a peak in June, but heterotrophs dominated throughout the year. Autotrophic biomass was mainly comprised by nanoflagellates and diatoms in the first half of the year, and by dinoflagellates and Synechococcus spp. in the second half. Heterotrophic biomass was mostly dominated by heterotrophic bacteria, followed by nanoflagellates and microzooplankton. Dilution experiments suggest that nano- and microzooplankton were significant consumers of autotrophs and heterotrophic bacteria. More than 100% of bacterial production was consumed by grazers in all experiments, while 46%, 21% and 30% of daily primary production were consumed in February, June and December, respectively. In February, autotrophs were the main carbon source, but in December, it was heterotrophic bacteria. An intermediate situation was observed in June, with similar carbon flows from autotrophs and heterotrophic bacteria. Size-fraction dilution experiments suggested that heterotrophic nanoflagellates are an important link between the high heterotrophic bacterial biomass and microzooplankton. In summary, these results indicate that nano- and microzooplankton were responsible for comprising a significant fraction of total microbial plankton biomass, standing stocks, growth and grazing processes. This suggests that in 2011, the microbial food web was an important compartment of the planktonic food web in the coastal southeastern Black Sea. Keywords: Phytoplankton, Microzooplankton, Carbon biomass, Microbial food web, Grazing, Black Sea

Effects of diurnal temperature variation on microbial community and petroleum hydrocarbon biodegradation in contaminated soils from a sub-Arctic site.

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Akbari, Ali; Ghoshal, Subhasis

2015-12-01

Contaminated soils are subject to diurnal and seasonal temperature variations during on-site ex-situ bioremediation processes. We assessed how diurnal temperature variations similar to that in summer at the site from which petroleum hydrocarbon-contaminated soil was collected affect the soil microbial community and the extent of biodegradation of petroleum hydrocarbons compared with constant temperature regimes. Microbial community analyses for 16S rRNA and alkB genes by pyrosequencing indicated that the microbial community for soils incubated under diurnal temperature variation from 5°C to 15°C (VART5-15) evolved similarly to that for soils incubated at constant temperature of 15°C (CST15). In contrast, under a constant temperature of 5°C (CST5), the community evolved significantly different. The extent of biodegradation of C10-C16 hydrocarbons in the VART5-15 systems was 48%, comparable with the 41% biodegradation in CST15 systems, but significantly higher than CST5 systems at 11%. The enrichment of Gammaproteobacteria was observed in the alkB gene-harbouring communities in VART5-15 and CST15 but not in CST5 systems. However, the Actinobacteria was abundant at all temperature regimes. The results suggest that changes in microbial community composition as a result of diurnal temperature variations can significantly influence petroleum hydrocarbon bioremediation performance in cold regions. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Shifts in microbial populations in Rusitec fermenters as affected by the type of diet and impact of the method for estimating microbial growth (15N v. microbial DNA).

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Mateos, I; Ranilla, M J; Saro, C; Carro, M D

2017-11-01

Rusitec fermenters are in vitro systems widely used to study ruminal fermentation, but little is known about the microbial populations establishing in them. This study was designed to assess the time evolution of microbial populations in fermenters fed medium- (MC; 50% alfalfa hay : concentrate) and high-concentrate diets (HC; 15 : 85 barley straw : concentrate). Samples from solid (SOL) and liquid (LIQ) content of fermenters were taken immediately before feeding on days 3, 8 and 14 of incubation for quantitative polymerase chain reaction and automated ribosomal intergenic spacer analysis analyses. In SOL, total bacterial DNA concentration and relative abundance of Ruminococcus flavefaciens remained unchanged over the incubation period, but protozoal DNA concentration and abundance of Fibrobacter succinogenes, Ruminococcus albus and fungi decreased and abundance of methanogenic archaea increased. In LIQ, total bacterial DNA concentration increased with time, whereas concentration of protozoal DNA and abundance of methanogens and fungi decreased. Diet×time interactions were observed for bacterial and protozoal DNA and relative abundance of F. succinogenes and R. albus in SOL, as well as for protozoal DNA in LIQ. Bacterial diversity in SOL increased with time, but no changes were observed in LIQ. The incubated diet influenced all microbial populations, with the exception of total bacteria and fungi abundance in LIQ. Bacterial diversity was higher in MC-fed than in HC-fed fermenters in SOL, but no differences were detected in LIQ. Values of pH, daily production of volatile fatty acids and CH4 and isobutyrate proportions remained stable over the incubation period, but other fermentation parameters varied with time. The relationships among microbial populations and fermentation parameters were in well agreement with those previously reported in in vivo studies. Using 15N as a microbial marker or quantifying total microbial DNA for estimating microbial protein synthesis

The microbial ecology of permafrost

DEFF Research Database (Denmark)

Jansson, Janet; Tas, Neslihan

2014-01-01

Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost......-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles....

Microbial contamination of drinking water from risky tubewells situated in different hydrological regions of Bangladesh.

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Dey, Nepal C; Parvez, Mahmood; Dey, Digbijoy; Saha, Ratnajit; Ghose, Lucky; Barua, Milan K; Islam, Akramul; Chowdhury, Mushtaque R

2017-05-01

This study, conducted in 40 selected upazilas covering four hydrological regions of Bangladesh, aimed at determining the risk of selected shallow tubewells (depthcontamination of shallow tubewells. The main objective of the study was to observe the seasonal and regional differences of microbial contamination and finally reaching a conclusion about safe distance between tubewells and latrines by comparing the contamination of two tubewell categories (category-1: distance ≤10m from nearest latrine; n=80 and category 2: distances 11-20m from nearest latrine; n=80) in different geographical contexts. About 62% of sampled tubewells were at medium to high risk according to WHO's sanitary inspection guidelines, while the situation was worst in south-west region. Microbiological contamination was significantly higher in sampled category-1 tubewells compared to category-2 tubewells, while the number of contaminated tubewells and level of contamination was higher during wet season. About 21% (CI 95 =12%-30%), 54% (CI 95 =43%-65%) and 58% (CI 95 =46%-69%) of water samples collected from category-1 tubewells were contaminated by E. coli, FC, and TC respectively during the wet season. The number of category-1 tubewells having E.coli was highest in the north-west (n=8) and north-central (n=4) region during wet season and dry season respectively, while the level of E.coli contamination in tubewell water (number of CFU/100ml of sample) was significantly higher in north-central region. However, the south-west region had the highest number of FC contaminated category-1 tubewells (n=16 & n=17; respectively during wet and dry season) and significantly a higher level of TC and FC in sampled Category-1 tubewells than north-west, north-central and south-east region, mainly during wet season. Multivariate regression analysis could identified some sanitary inspection indicators, such as tubewell within contaminants in tubewell water (pcontamination. Construction of pit latrine in areas

Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region.

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Bevivino, Annamaria; Paganin, Patrizia; Bacci, Giovanni; Florio, Alessandro; Pellicer, Maite Sampedro; Papaleo, Maria Cristiana; Mengoni, Alessio; Ledda, Luigi; Fani, Renato; Benedetti, Anna; Dalmastri, Claudia

2014-01-01

Land-use change is considered likely to be one of main drivers of biodiversity changes in grassland ecosystems. To gain insight into the impact of land use on the underlying soil bacterial communities, we aimed at determining the effects of agricultural management, along with seasonal variations, on soil bacterial community in a Mediterranean ecosystem where different land-use and plant cover types led to the creation of a soil and vegetation gradient. A set of soils subjected to different anthropogenic impact in a typical Mediterranean landscape, dominated by Quercus suber L., was examined in spring and autumn: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards (ploughed and grass covered). Land uses affected the chemical and structural composition of the most stabilised fractions of soil organic matter and reduced soil C stocks and labile organic matter at both sampling season. A significant effect of land uses on bacterial community structure as well as an interaction effect between land uses and season was revealed by the EP index. Cluster analysis of culture-dependent DGGE patterns showed a different seasonal distribution of soil bacterial populations with subgroups associated to different land uses, in agreement with culture-independent T-RFLP results. Soils subjected to low human inputs (cork-oak forest and pasture) showed a more stable bacterial community than those with high human input (vineyards and managed meadow). Phylogenetic analysis revealed the predominance of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes phyla with differences in class composition across the site, suggesting that the microbial composition changes in response to land uses. Taken altogether, our data suggest that soil bacterial communities were seasonally distinct and exhibited compositional shifts that tracked with changes in land use and soil management. These findings may contribute to future searches for bacterial bio-indicators of soil

Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region.

Directory of Open Access Journals (Sweden)

Annamaria Bevivino

Full Text Available Land-use change is considered likely to be one of main drivers of biodiversity changes in grassland ecosystems. To gain insight into the impact of land use on the underlying soil bacterial communities, we aimed at determining the effects of agricultural management, along with seasonal variations, on soil bacterial community in a Mediterranean ecosystem where different land-use and plant cover types led to the creation of a soil and vegetation gradient. A set of soils subjected to different anthropogenic impact in a typical Mediterranean landscape, dominated by Quercus suber L., was examined in spring and autumn: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards (ploughed and grass covered. Land uses affected the chemical and structural composition of the most stabilised fractions of soil organic matter and reduced soil C stocks and labile organic matter at both sampling season. A significant effect of land uses on bacterial community structure as well as an interaction effect between land uses and season was revealed by the EP index. Cluster analysis of culture-dependent DGGE patterns showed a different seasonal distribution of soil bacterial populations with subgroups associated to different land uses, in agreement with culture-independent T-RFLP results. Soils subjected to low human inputs (cork-oak forest and pasture showed a more stable bacterial community than those with high human input (vineyards and managed meadow. Phylogenetic analysis revealed the predominance of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes phyla with differences in class composition across the site, suggesting that the microbial composition changes in response to land uses. Taken altogether, our data suggest that soil bacterial communities were seasonally distinct and exhibited compositional shifts that tracked with changes in land use and soil management. These findings may contribute to future searches for bacterial bio

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

Science.gov (United States)

Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

2014-01-01

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

Microbial community structures in high rate algae ponds for bioconversion of agricultural wastes from livestock industry for feed production.

Science.gov (United States)

Mark Ibekwe, A; Murinda, Shelton E; Murry, Marcia A; Schwartz, Gregory; Lundquist, Trygve

2017-02-15

Dynamics of seasonal microbial community compositions in algae cultivation ponds are complex. However, there is very limited knowledge on bacterial communities that may play significant roles with algae in the bioconversion of manure nutrients to animal feed. In this study, water samples were collected during winter, spring, summer, and fall from the dairy lagoon effluent (DLE), high rate algae ponds (HRAP) that were fed with diluted DLE, and municipal waste water treatment plant (WWTP) effluent which was included as a comparison system for the analysis of total bacteria, Cyanobacteria, and microalgae communities using MiSeq Illumina sequencing targeting the 16S V4 rDNA region. The main objective was to examine dynamics in microbial community composition in the HRAP used for the production of algal biomass. DNA was extracted from the different sample types using three commercially available DNA extraction kits; MoBio Power water extraction kit, Zymo fungi/bacterial extraction kit, and MP Biomedicals FastDNA SPIN Kit. Permutational analysis of variance (PERMANOVA) using distance matrices on each variable showed significant differences (P=0.001) in beta-diversity based on sample source. Environmental variables such as hydraulic retention time (HRT; P<0.031), total N (P<0.002), total inorganic N (P<0.002), total P (P<0.002), alkalinity (P<0.002), pH (P<0.022), total suspended solid (TSS; P<0.003), and volatile suspended solids (VSS; P<0.002) significantly affected microbial communities in DLE, HRAP, and WWTP. Of the operational taxonomic units (OTUs) identified to phyla level, the dominant classes of bacteria identified were: Cyanobacteria, Alpha-, Beta-, Gamma-, Epsilon-, and Delta-proteobacteria, Bacteroidetes, Firmicutes, and Planctomycetes. Our data suggest that microbial communities were significantly affected in HRAP by different environmental variables, and care must be taken in extraction procedures when evaluating specific groups of microbial communities for

Contributions of microbial activity and ash deposition to post-fire nitrogen availability in a pine savanna

Science.gov (United States)

Ficken, Cari D.; Wright, Justin P.

2017-01-01

Many ecosystems experience drastic changes to soil nutrient availability associated with fire, but the magnitude and duration of these changes are highly variable among vegetation and fire types. In pyrogenic pine savannas across the southeastern United States, pulses of soil inorganic nitrogen (N) occur in tandem with ecosystem-scale nutrient losses from prescribed burns. Despite the importance of this management tool for restoring and maintaining fire-dependent plant communities, the contributions of different mechanisms underlying fire-associated changes to soil N availability remain unclear. Pulses of N availability following fire have been hypothesized to occur through (1) changes to microbial cycling rates and (2) direct ash deposition. Here, we document fire-associated changes to N availability across the growing season in a longleaf pine savanna in North Carolina. To differentiate between possible mechanisms driving soil N pulses, we measured net microbial cycling rates and changes to soil δ15N before and after a burn. Our findings refute both proposed mechanisms: we found no evidence for changes in microbial activity, and limited evidence that ash deposition could account for the increase in ammonium availability to more than 5-25 times background levels. Consequently, we propose a third mechanism to explain post-fire patterns of soil N availability, namely that (3) changes to plant sink strength may contribute to ephemeral increases in soil N availability, and encourage future studies to explicitly test this mechanism.

Phosphorus fractions, microbial biomass and enzyme activities in ...

African Journals Online (AJOL)

Potohar, northern Punjab, Pakistan in September, 2008 and analysed for P fractions and microbial parameters including microbial biomass C, microbial biomass N, microbial biomass P, and activities of dehydrogenase and alkaline phosphatase enzymes. The average size of different P fractions (% of total P) in the soils ...

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

Science.gov (United States)

Bernard, Guillaume; Pathmanathan, Jananan S; Lannes, Romain; Lopez, Philippe; Bapteste, Eric

2018-01-01

Abstract Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns. PMID:29420719

Microbial biofilms: biosurfactants as antibiofilm agents.

Science.gov (United States)

Banat, Ibrahim M; De Rienzo, Mayri A Díaz; Quinn, Gerry A

2014-12-01

Current microbial inhibition strategies based on planktonic bacterial physiology have been known to have limited efficacy on the growth of biofilm communities. This problem can be exacerbated by the emergence of increasingly resistant clinical strains. All aspects of biofilm measurement, monitoring, dispersal, control, and inhibition are becoming issues of increasing importance. Biosurfactants have merited renewed interest in both clinical and hygienic sectors due to their potential to disperse microbial biofilms in addition to many other advantages. The dispersal properties of biosurfactants have been shown to rival those of conventional inhibitory agents against bacterial and yeast biofilms. This makes them suitable candidates for use in new generations of microbial dispersal agents and for use as adjuvants for existing microbial suppression or eradication strategies. In this review, we explore aspects of biofilm characteristics and examine the contribution of biologically derived surface-active agents (biosurfactants) to the disruption or inhibition of microbial biofilms.

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence

KAUST Repository

Pearman, John K.; Ellis, Joanne; Irigoien, Xabier; Yellepeddi, Sarma B.; Jones, Burton; Carvalho, Susana

2017-01-01

The semi-enclosed nature of the Red Sea (20.2°N-38.5°N) makes it a natural laboratory to study the influence of environmental gradients on microbial communities. This study investigates the composition and structure of microbial prokaryotes and eukaryotes using molecular methods, targeting ribosomal RNA genes across different regions and seasons. The interaction between spatial and temporal scales results in different scenarios of turbulence and nutrient conditions allowing for testing of ecological theory that categorizes the response of the plankton community to these variations. The prokaryotic reads are mainly comprised of Cyanobacteria and Proteobacteria (Alpha and Gamma), with eukaryotic reads dominated by Dinophyceae and Syndiniophyceae. Periodic increases in the proportion of Mamiellophyceae and Bacillariophyceae reads were associated with alterations in the physical oceanography leading to nutrient increases either through the influx of Gulf of Aden Intermediate Water (south in the fall) or through water column mixing processes (north in the spring). We observed that in general dissimilarity amongst microbial communities increased when nutrient concentrations were higher, whereas richness (observed OTUs) was higher in scenarios of higher turbulence. Maximum abundance models showed the differential responses of dominant taxa to temperature giving an indication how taxa will respond as waters become warmer and more oligotrophic.

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence

KAUST Repository

Pearman, John K.

2017-07-20

The semi-enclosed nature of the Red Sea (20.2°N-38.5°N) makes it a natural laboratory to study the influence of environmental gradients on microbial communities. This study investigates the composition and structure of microbial prokaryotes and eukaryotes using molecular methods, targeting ribosomal RNA genes across different regions and seasons. The interaction between spatial and temporal scales results in different scenarios of turbulence and nutrient conditions allowing for testing of ecological theory that categorizes the response of the plankton community to these variations. The prokaryotic reads are mainly comprised of Cyanobacteria and Proteobacteria (Alpha and Gamma), with eukaryotic reads dominated by Dinophyceae and Syndiniophyceae. Periodic increases in the proportion of Mamiellophyceae and Bacillariophyceae reads were associated with alterations in the physical oceanography leading to nutrient increases either through the influx of Gulf of Aden Intermediate Water (south in the fall) or through water column mixing processes (north in the spring). We observed that in general dissimilarity amongst microbial communities increased when nutrient concentrations were higher, whereas richness (observed OTUs) was higher in scenarios of higher turbulence. Maximum abundance models showed the differential responses of dominant taxa to temperature giving an indication how taxa will respond as waters become warmer and more oligotrophic.

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

Energy Technology Data Exchange (ETDEWEB)

Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

2015-05-29

Modern microbial mats are potential analogues of some of Earth’s earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic nextgeneration sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.

Influences of seasons, N/P ratios and chemical compounds on phosphorus removal performance in algal pond combined with constructed wetlands.

Science.gov (United States)

Zhimiao, Zhao; Xinshan, Song; Yanping, Xiao; Yufeng, Zhao; Zhijie, Gong; Fanda, Lin; Yi, Ding; Wei, Wang; Tianling, Qin

2016-12-15

Nitrogen (N) and phosphorous (P) are main contaminants and P removal was restrained by several factors: season, N/P, and chemical compounds (CCs) in water ecosystems. In this paper, two algal ponds combined with constructed wetlands were built to increase the removal performance. Different hydraulic retention time (HRT), different N/P and chemical compounds were chosen to investigate the influences of the above factors on the contaminant removal performance. The optimum phosphorus removal rate was 69.74% under the nitrogen removal of 92.85% in influent containing PO 4 3- after 3-day HRT in algal pond combined with constructed wetlands. The investigation results indicated that these factors improved the nutrient removal efficiencies. Seasonal influence on the removal performance can be avoided by choosing the optimal HRT length of 3days. The higher N/P at 60 can improve the phosphorus removal and the lower N/P at 15 showed the stronger synergistic effect between phosphorus and nitrogen removals. Compared with PO 3 - and P 2 O 7 4- in influent, PO 4 3- affected phosphorus removal more significantly. The better linear fitting between organic phosphorus removal and nitrogen removal in influent contained P 2 O 7 4- was found. Algae can absorb nutrients for growth, and oxygen release, microbial activity intensification and microbial carbon replenishment induced by algae will improve the performance. The study suggested that the control of HRTs, N/Ps, CCs, and algae might be an effective way to improve wastewater treatment performance. Copyright © 2016 Elsevier B.V. All rights reserved.

The Impact of Human Activities on Microbial Quality of Rivers in the Vhembe District, South Africa

Directory of Open Access Journals (Sweden)

Afsatou N. Traoré

2016-08-01

Full Text Available Background: Water quality testing is dictated by microbial agents found at the time of sampling in reference to their acceptable risk levels. Human activities might contaminate valuable water resources and add to the microbial load present in water bodies. Therefore, the effects of human activities on the microbial quality of rivers collected from twelve catchments in the Vhembe District in South Africa were investigated, with samples analyzed for total coliform (TC and Eschericha coli (E. coli contents. Methods: Physical parameters and various human activities were recorded for each sampling site. The Quanti-Tray® method was adopted for the assessment of TC and E. coli contents in the rivers over a two-year period. A multiplex polymerase chain (PCR method was used to characterize the strains of E. coli found. Results: The microbial quality of the rivers was poor with both TC and E. coli contents found to be over acceptable limits set by the South African Department of Water and Sanitation (DWS. No significant difference (p > 0.05 was detected between TC and E. coli risks in dry and wet seasons. All six pathogenic E. coli strains were identified and Enteroaggregative E. coli (EAEC, atypical Enteropathogenic E. coli (a-EPEC and Enterotoxigenic E. coli (ETEC were the most prevalent E. coli strains detected (respectively, 87%, 86% and 83%. Conclusions: The study indicated that contamination in the majority of sampling sites, due to human activities such as car wash, animal grazing and farming, poses health risks to communities using the rivers for various domestic chores. It is therefore recommended that more education by the respective departments is done to avert pollution of rivers and prevent health risks to the communities in the Vhembe District.

Microbial ecology of phototrophic biofilms

NARCIS (Netherlands)

Roeselers, G.

2007-01-01

Biofilms are layered structures of microbial cells and an extracellular matrix of polymeric substances, associated with surfaces and interfaces. Biofilms trap nutrients for growth of the enclosed microbial community and help prevent detachment of cells from surfaces in flowing systems. Phototrophic

Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques

Directory of Open Access Journals (Sweden)

Anna Gałązka

2018-01-01

Full Text Available Fungal diversity in the soil may be limited under natural conditions by inappropriate environmental factors such as: nutrient resources, biotic and abiotic factors, tillage system and microbial interactions that prevent the occurrence or survival of the species in the environment. The aim of this paper was to determine fungal genetic diversity and community level physiological profiling of microbial communities in the soil under long-term maize monoculture. The experimental scheme involved four cultivation techniques: direct sowing (DS, reduced tillage (RT, full tillage (FT, and crop rotation (CR. Soil samples were taken in two stages: before sowing of maize (DSBS-direct sowing, RTBS-reduced tillage, FTBS-full tillage, CRBS-crop rotation and the flowering stage of maize growth (DSF-direct sowing, RTF-reduced tillage, FTF-full tillage, CRF-crop rotation. The following plants were used in the crop rotation: spring barley, winter wheat and maize. The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, the season had a great influence on the fungal genetic structure in the soil. Significant differences were found on the family level (P = 0.032, F = 3.895, genus level (P = 0.026, F = 3.313 and on the species level (P = 0.033, F = 2.718. This study has shown that: (1 fungal diversity was changed

Microbial Character Related Sulfur Cycle under Dynamic Environmental Factors Based on the Microbial Population Analysis in Sewerage System.

Science.gov (United States)

Dong, Qian; Shi, Hanchang; Liu, Yanchen

2017-01-01

The undesired sulfur cycle derived by microbial population can ultimately causes the serious problems of sewerage systems. However, the microbial community characters under dynamic environment factors in actual sewerage system is still not enough. This current study aimed to character the distributions and compositions of microbial communities that participate in the sulfur cycle under the dynamic environmental conditions in a local sewerage system. To accomplish this, microbial community compositions were assessed using 454 high-throughput sequencing (16S rDNA) combined with dsrB gene-based denaturing gradient gel electrophoresis. The results indicated that a higher diversity of microbial species was present at locations in sewers with high concentrations of H 2 S. Actinobacteria and Proteobacteria were dominant in the sewerage system, while Actinobacteria alone were dominant in regions with high concentrations of H 2 S. Specifically, the unique operational taxonomic units could aid to characterize the distinct microbial communities within a sewerage manhole. The proportion of sulfate-reducing bacteria, each sulfur-oxidizing bacteria (SOB) were strongly correlated with the liquid parameters (DO, ORP, COD, Sulfide, NH 3 -N), while the Mycobacterium and Acidophilic SOB (M&A) was strongly correlated with gaseous factors within the sewer, such as H 2 S, CH 4 , and CO. Identifying the distributions and proportions of critical microbial communities within sewerage systems could provide insights into how the microbial sulfur cycle is affected by the dynamic environmental conditions that exist in sewers and might be useful for explaining the potential sewerage problems.

Seasonal and Non-Seasonal Generalized Pareto Distribution to Estimate Extreme Significant Wave Height in The Banda Sea

Science.gov (United States)

Nursamsiah; Nugroho Sugianto, Denny; Suprijanto, Jusup; Munasik; Yulianto, Bambang

2018-02-01

The information of extreme wave height return level was required for maritime planning and management. The recommendation methods in analyzing extreme wave were better distributed by Generalized Pareto Distribution (GPD). Seasonal variation was often considered in the extreme wave model. This research aims to identify the best model of GPD by considering a seasonal variation of the extreme wave. By using percentile 95 % as the threshold of extreme significant wave height, the seasonal GPD and non-seasonal GPD fitted. The Kolmogorov-Smirnov test was applied to identify the goodness of fit of the GPD model. The return value from seasonal and non-seasonal GPD was compared with the definition of return value as criteria. The Kolmogorov-Smirnov test result shows that GPD fits data very well both seasonal and non-seasonal model. The seasonal return value gives better information about the wave height characteristics.

Response of soil microbial activities and microbial community structure to vanadium stress.

Science.gov (United States)

Xiao, Xi-Yuan; Wang, Ming-Wei; Zhu, Hui-Wen; Guo, Zhao-Hui; Han, Xiao-Qing; Zeng, Peng

2017-08-01

High levels of vanadium (V) have long-term, hazardous impacts on soil ecosystems and biological processes. In the present study, the effects of V on soil enzymatic activities, basal respiration (BR), microbial biomass carbon (MBC), and the microbial community structure were investigated through 12-week greenhouse incubation experiments. The results showed that V content affected soil dehydrogenase activity (DHA), BR, and MBC, while urease activity (UA) was less sensitive to V stress. The average median effective concentration (EC 50 ) thresholds of V were predicted using a log-logistic dose-response model, and they were 362mgV/kg soil for BR and 417mgV/kg soil for DHA. BR and DHA were more sensitive to V addition and could be used as biological indicators for soil V pollution. According to a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, the structural diversity of the microbial community decreased for soil V contents ranged between 254 and 1104mg/kg after 1 week of incubation. As the incubation time increased, the diversity of the soil microbial community structure increased for V contents ranged between 354 and 1104mg/kg, indicating that some new V-tolerant bacterial species might have replicated under these conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

Microbially produced phytotoxins and plant disease management ...

African Journals Online (AJOL)

Nowadays, these evaluation techniques are becoming an important complement to classical breeding methods. The knowledge of the inactivation of microbial toxins has led to the use of microbial enzymes to inactivate phytotoxins thereby reducing incidence and severity of disease induced by microbial toxins. Considering ...

Anode microbial communities produced by changing from microbial fuel cell to microbial electrolysis cell operation using two different wastewaters

KAUST Repository

Kiely, Patrick D.; Cusick, Roland; Call, Douglas F.; Selembo, Priscilla A.; Regan, John M.; Logan, Bruce E.

2011-01-01

Conditions in microbial fuel cells (MFCs) differ from those in microbial electrolysis cells (MECs) due to the intrusion of oxygen through the cathode and the release of H2 gas into solution. Based on 16S rRNA gene clone libraries, anode communities in reactors fed acetic acid decreased in species richness and diversity, and increased in numbers of Geobacter sulfurreducens, when reactors were shifted from MFCs to MECs. With a complex source of organic matter (potato wastewater), the proportion of Geobacteraceae remained constant when MFCs were converted into MECs, but the percentage of clones belonging to G. sulfurreducens decreased and the percentage of G. metallireducens clones increased. A dairy manure wastewater-fed MFC produced little power, and had more diverse microbial communities, but did not generate current in an MEC. These results show changes in Geobacter species in response to the MEC environment and that higher species diversity is not correlated with current. © 2010 Elsevier Ltd.

Seasonal Variation in Group Size Is Related to Seasonal Variation in Neuropeptide Receptor Density.

Science.gov (United States)

Wilson, Leah C; Goodson, James L; Kingsbury, Marcy A

2016-01-01

In many species, seasonal variation in grouping behavior is widespread, with shifts towards territoriality in the breeding season and grouping in the winter. Compared to the hormonal and neural mechanisms of seasonal territorial aggression, the mechanisms that promote seasonal grouping have received little attention. We collected brains in spring and winter from wild-caught males of two species of emberizid sparrows that seasonally flock (the field sparrow, Spizella pusilla, and the dark-eyed junco, Junco hyemalis) and two species that do not seasonally flock (the song sparrow, Melospiza melodia, and the eastern towhee, Pipilo erythrophthalmus). We used receptor autoradiography to quantify seasonal plasticity in available binding sites for three neuropeptides known to influence social behavior. We examined binding sites for 125I-vasoactive intestinal polypeptide (VIP), 125I-sauvagine (SG, a ligand for corticotropin-releasing hormone receptors) and 125I-ornithine vasotocin analog (OVTA, a ligand for the VT3 nonapeptide). For all species and ligands, brain areas that exhibited a seasonal pattern in binding density were characterized by a winter increase. Compared to nonflocking species, seasonally flocking species showed different binding patterns in multiple brain areas. Furthermore, we found that winter flocking was associated with elevated winter 125I-VIP binding density in the medial amygdala, as well as 125I-VIP and 125I-OVTA binding density in the rostral arcopallium. While the functional significance of the avian rostral arcopallium is unclear, it may incorporate parts of the pallial amygdala. Our results point to this previously undescribed area as a likely hot spot of social modulation. © 2016 S. Karger AG, Basel.

Seasonal Variations in Color Preference.

Science.gov (United States)

Schloss, Karen B; Nelson, Rolf; Parker, Laura; Heck, Isobel A; Palmer, Stephen E

2017-08-01

We investigated how color preferences vary according to season and whether those changes could be explained by the ecological valence theory (EVT). To do so, we assessed the same participants' preferences for the same colors during fall, winter, spring, and summer in the northeastern United States, where there are large seasonal changes in environmental colors. Seasonal differences were most pronounced between fall and the other three seasons. Participants liked fall-associated dark-warm colors-for example, dark-red, dark-orange (brown), dark-yellow (olive), and dark-chartreuse-more during fall than other seasons. The EVT could explain these changes with a modified version of Palmer and Schloss' (2010) weighted affective valence estimate (WAVE) procedure that added an activation term to the WAVE equation. The results indicate that color preferences change according to season, as color-associated objects become more/less activated in the observer. These seasonal changes in color preferences could not be characterized by overall shifts in weights along cone-contrast axes. Copyright © 2016 Cognitive Science Society, Inc.

Comparing microbial water quality in an intermittent and continuous piped water supply.

Science.gov (United States)

Kumpel, Emily; Nelson, Kara L

2013-09-15

Supplying piped water intermittently is a common practice throughout the world that increases the risk of microbial contamination through multiple mechanisms. Converting an intermittent supply to a continuous supply has the potential to improve the quality of water delivered to consumers. To understand the effects of this upgrade on water quality, we tested samples from reservoirs, consumer taps, and drinking water provided by households (e.g. from storage containers) from an intermittent and continuous supply in Hubli-Dharwad, India, over one year. Water samples were tested for total coliform, Escherichia coli, turbidity, free chlorine, and combined chlorine. While water quality was similar at service reservoirs supplying the continuous and intermittent sections of the network, indicator bacteria were detected more frequently and at higher concentrations in samples from taps supplied intermittently compared to those supplied continuously (p supply, with 0.7% of tap samples positive compared to 31.7% of intermittent water supply tap samples positive for E. coli. In samples from both continuously and intermittently supplied taps, higher concentrations of total coliform were measured after rainfall events. While source water quality declined slightly during the rainy season, only tap water from intermittent supply had significantly more indicator bacteria throughout the rainy season compared to the dry season. Drinking water samples provided by households in both continuous and intermittent supplies had higher concentrations of indicator bacteria than samples collected directly from taps. Most households with continuous supply continued to store water for drinking, resulting in re-contamination, which may reduce the benefits to water quality of converting to continuous supply. Copyright © 2013 Elsevier Ltd. All rights reserved.

Seasonal difference in brain serotonin transporter binding predicts symptom severity in patients with seasonal affective disorder

DEFF Research Database (Denmark)

Mc Mahon, Brenda; Andersen, Sofie B.; Madsen, Martin K.

2016-01-01

controls with low seasonality scores and 17 patients diagnosed with seasonal affective disorder were scanned in both summer and winter to investigate differences in cerebral serotonin transporter binding across groups and across seasons. The two groups had similar cerebral serotonin transporter binding...... between summer and winter (Psex-(P = 0.02) and genotype-(P = 0.04) dependent. In the patients with seasonal affective disorder, the seasonal change in serotonin transporter binding was positively associated with change in depressive symptom...

Statistical Physics Approaches to Microbial Ecology

Science.gov (United States)

Mehta, Pankaj

The unprecedented ability to quantitatively measure and probe complex microbial communities has renewed interest in identifying the fundamental ecological principles governing community ecology in microbial ecosystems. Here, we present work from our group and others showing how ideas from statistical physics can help us uncover these ecological principles. Two major lessons emerge from this work. First, large, ecosystems with many species often display new, emergent ecological behaviors that are absent in small ecosystems with just a few species. To paraphrase Nobel laureate Phil Anderson, ''More is Different'', especially in community ecology. Second, the lack of trophic layer separation in microbial ecology fundamentally distinguishes microbial ecology from classical paradigms of community ecology and leads to qualitative different rules for community assembly in microbes. I illustrate these ideas using both theoretical modeling and novel new experiments on large microbial ecosystems performed by our collaborators (Joshua Goldford and Alvaro Sanchez). Work supported by Simons Investigator in MMLS and NIH R35 R35 GM119461.

Microbial degradation and impact of Bracken toxin ptaquiloside on microbial communities in soil

DEFF Research Database (Denmark)

Engel, Pernille; Brandt, Kristian Koefoed; Rasmussen, Lars Holm

2007-01-01

), but not in the NZ soil (weak acid loamy Entisol). In the DK soil PTA turnover was predominantly due to microbial degradation (biodegradation); chemical hydrolysis was occurring mainly in the uppermost A horizon where pH was very low (3.4). Microbial activity (basal respiration) and growth ([3H]leucine incorporation...... assay) increased after PTA exposure, indicating that the Bracken toxin served as a C substrate for the organotrophic microorganisms. On the other hand, there was no apparent impact of PTA on community size as measured by substrate-induced respiration or composition as indicated by community......-level physiological profiles. Our results demonstrate that PTA stimulates microbial activity and that microorganisms play a predominant role for rapid PTA degradation in Bracken-impacted soils....

Microbial Endocrinology: An Ongoing Personal Journey.

Science.gov (United States)

Lyte, Mark

2016-01-01

The development of microbial endocrinology is covered from a decidedly personal perspective. Specific focus is given to the role of microbial endocrinology in the evolutionary symbiosis between man and microbe as it relates to both health and disease. Since the first edition of this book series 5 years ago, the role of microbial endocrinology in the microbiota-gut-brain axis is additionally discussed. Future avenues of research are suggested.

Seasonality of major redox constituents in a shallow subterranean estuary

Science.gov (United States)

O'Connor, Alison E.; Krask, Julie L.; Canuel, Elizabeth A.; Beck, Aaron J.

2018-03-01

The subterranean estuary (STE), the subsurface mixing zone of outflowing fresh groundwater and infiltrating seawater, is an area of extensive geochemical reactions that determine the composition of groundwater that flows into coastal environments. This study examined the porewater composition of a shallow STE (redox gradients on STE geochemistry. Two freshwater endmembers were identified, between which redox potential and composition varied with depth-a shallow freshwater endmember was oxidizing and high in DOC, whereas a deep freshwater endmember was reducing, lower in DOC, and high in sulfide. Results showed that dissolved Fe, Mn, and sulfide varied along a redox gradient distinct from the salinity gradient, and that three-endmember mixing was required to quantify non-conservative chemical addition/removal in the STE. In addition to salinity, humic carbon was used as a quasi-conservative tracer to quantify mixing according to a three-endmember model. The vertical distributions of DOC and reduced metabolites remained approximately constant over time, but concentrations varied with season. Dissolved organic carbon concentrations were greatest in the summer, and shallow meteoric groundwater supplied the majority of DOC to the STE. In summer, there was additional evidence for shallow non-conservative addition of DOC. Dissolved Fe and Mn were highest in a subsurface plume through the middle of the STE (100-140 cm below sediment surface at the high tide line) which was characterized by higher concentrations and greater non-conservative addition in the winter. In contrast, sulfide was higher in summer at depths within the Fe and Mn plume (100-140 cm). We attribute the contrasting seasonal patterns of dissolved Fe, Mn, and sulfide to differences in microbial response to temperature changes and organic matter availability, and to competition at the ferrous-sulfidic transition zone between dissimilatory metal reduction and sulfate reduction, leading to sulfate

The Role of Soil Organic Matter, Nutrients, and Microbial Community Structure on the Performance of Microbial Fuel Cells

Science.gov (United States)

Rooney-Varga, J. N.; Dunaj, S. J.; Vallino, J. J.; Hines, M. E.; Gay, M.; Kobyljanec, C.

2011-12-01

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful, natural, and renewable resource: soil organic carbon. In the current study, we analyzed microbial community structure, MFC performance, and soil characteristics in different microhabitats (bulk soil, anode, and cathode) within MFCs constructed from agricultural or forest soils in order to determine how soil type and microbial dynamics influence MFC performance. MFCs were constructed with soils from agricultural and hardwood forest sites at Harvard Forest (Petersham, MA). The bulk soil characteristics were analyzed, including polyphenols, short chain fatty acids, total organic C and N, abiotic macronutrients, N and P mineralization rates, CO2 respiration rates, and MFC power output. Microbial community structure of the anodes, cathodes, and bulk soils was determined with molecular fingerprinting methods, which included terminal restriction length polymorphism (T-RFLP) analysis and 16S rRNA gene sequencing analysis. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs, suggesting that active agricultural MFC microbial communities were supported by higher quality organic carbon. Microbial community profile data indicate that the microbial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and, to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These data suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic microbial

Performance and microbial community structure of a polar Arctic Circle aerobic granular sludge system operating at low temperature.

Science.gov (United States)

Gonzalez-Martinez, Alejandro; Muñoz-Palazon, Barbara; Maza-Márquez, Paula; Rodriguez-Sanchez, Alejandro; Gonzalez-Lopez, Jesus; Vahala, Riku

2018-05-01

The aim of this work was to study the performance and microbial community structure of a polar Arctic Circle aerobic granular sludge (AGS) system operating at low temperature. Thus, an AGS bioreactor was operated at 7, 5 and 3 °C of temperature using a cold-adapted sludge from Lapland. At 5 °C, it yielded acceptable conversion rates, in terms of nitrogen, phosphorous, and organic matter. However, under 3 °C a negligible nitrogen and phosphorous removal performance was observed. Below 5 °C, scanning electron microscopy studies showed a wispy, non-dense and irregular granular structure with a strong outgrowth of filamentous. Moreover, Illumina next-generation sequencing showed a heterogeneous microbial population where SM1K20 (Archaea), Trichosporon domesticum (Fungus), and Zooglea, Arcobacter and Acinetobacter (Bacteria) were the dominant phylotypes. Our study suggests that AGS technologies inoculated with North Pole sludge could be operated, in cold regions for a period longer than 3 months (winter season) under 5 °C of water temperature. Copyright © 2018 Elsevier Ltd. All rights reserved.

Synthetic Electric Microbial Biosensors

Science.gov (United States)

2017-06-10

domains and DNA-binding domains into a single protein for deregulation of down stream genes of have been favored [10]. Initially experiments with... Germany DISTRIBUTION A. Approved for public release: distribution unlimited.   Talk title: “Synthetic biology based microbial biosensors for the...toolbox” in Heidelberg, Germany Poster title: “Anaerobic whole cell microbial biosensors” Link: http://phdsymposium.embl.org/#home   September, 2014

Stay connected: Electrical conductivity of microbial aggregates.

Science.gov (United States)

Li, Cheng; Lesnik, Keaton Larson; Liu, Hong

2017-11-01

The discovery of direct extracellular electron transfer offers an alternative to the traditional understanding of diffusional electron exchange via small molecules. The establishment of electronic connections between electron donors and acceptors in microbial communities is critical to electron transfer via electrical currents. These connections are facilitated through conductivity associated with various microbial aggregates. However, examination of conductivity in microbial samples is still in its relative infancy and conceptual models in terms of conductive mechanisms are still being developed and debated. The present review summarizes the fundamental understanding of electrical conductivity in microbial aggregates (e.g. biofilms, granules, consortia, and multicellular filaments) highlighting recent findings and key discoveries. A greater understanding of electrical conductivity in microbial aggregates could facilitate the survey for additional microbial communities that rely on direct extracellular electron transfer for survival, inform rational design towards the aggregates-based production of bioenergy/bioproducts, and inspire the construction of new synthetic conductive polymers. Copyright © 2017 Elsevier Inc. All rights reserved.

Off-season biogenic volatile organic compound emissions from heath mesocosms: responses to vegetation cutting.

Science.gov (United States)

Rinnan, Riikka; Gierth, Diana; Bilde, Merete; Rosenørn, Thomas; Michelsen, Anders

2013-01-01

Biogenic volatile organic compounds (BVOCs) affect both atmospheric processes and ecological interactions. Our primary aim was to differentiate between BVOC emissions from above- and belowground plant parts and heath soil outside the growing season. The second aim was to assess emissions from herbivory, mimicked by cutting the plants. Mesocosms from a temperate Deschampsia flexuosa-dominated heath ecosystem and a subarctic mixed heath ecosystem were either left intact, the aboveground vegetation was cut, or all plant parts (including roots) were removed. For 3-5 weeks, BVOC emissions were measured in growth chambers by an enclosure method using gas chromatography-mass spectrometry. CO2 exchange, soil microbial biomass, and soil carbon and nitrogen concentrations were also analyzed. Vegetation cutting increased BVOC emissions by more than 20-fold, and the induced compounds were mainly eight-carbon compounds and sesquiterpenes. In the Deschampsia heath, the overall low BVOC emissions originated mainly from soil. In the mixed heath, root, and soil emissions were negligible. Net BVOC emissions from roots and soil of these well-drained heaths do not significantly contribute to ecosystem emissions, at least outside the growing season. If insect outbreaks become more frequent with climate change, ecosystem BVOC emissions will periodically increase due to herbivory.

Biodiversity and Seasonal Changes of the Microbiome in Chernozem Agroecosystem

Science.gov (United States)

Kutovaya, Olga; Chernov, Timofey; Tkhakakhova, Azida; Ivanova, Ekaterina

2016-04-01

Studies of the influence of different agricultural technologies on the soil microbiome are widespread; they are important for understanding the dependence of the microbiome on environmental and soil factors and solution of practical problems related to the control of biochemical processes in soils used in agriculture. The seasonal variability (spring-summer-autumn) of the taxonomic structure of prokaryotic microbiomes in chernozems was studied using sequencing of the 16S rRNA gene. The DNA preparation was used as the matrix for a polymerase chain reaction with the use of a pair of universal primers to the variable region V4 of the 16S rRNA gene - F515 (GTGCCAGCMGCCGCGGTAA) and R806 (GGACTACVSGGGTATCTAAT). The preparation of the samples and sequencing were made on a GS Junior. The samples were collected from the topsoil (0-20 cm) horizons of a long-term fallow and croplands differing in the rates of application of mineral fertilizers (NPK). The results of the weighted UniFrac analysis show that the microbiomes of the fallow and field were distinctly distinguished and that the type of land use significantly affected the structure of the microbial community. The most sensitive to the type of land use were the representatives of the Firmicutes, Gemmatiomonades, and Verrucomicrobia phyla. The type of vegetation and aeration of the root-dwelling soil layer seem to be key factors of this influence. The microbiomes analyzed also differed by seasons: in the autumn samples, they were closer to the spring ones than to the summer ones. This fact evidences that the seasonal differences in the microbiomes are not simple gradual temporal changes; they reflect the influence of some ecological factors transforming the phylogenetic structure of prokaryotic communities. As the seasonal shift was equally expressed in the microbiomes of the field and fallow, it is logical to assume that it was caused by the factors common for two systems of land use. Statistically sensitive to seasonal

Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

Directory of Open Access Journals (Sweden)

Florine Degrune

2017-06-01

Full Text Available Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Plowing is a fundamental component of conventional farming, but long-term detrimental effects such as soil erosion and loss of soil organic matter have been recognized. Moving towards more sustainable management practices such as reduced tillage or crop residue retention can reduce these detrimental effects, but will also influence structure and function of the soil microbiota with direct consequences for the associated ecosystem services. Although there is increasing evidence that different tillage regimes alter the soil microbiome, we have a limited understanding of the temporal dynamics of these effects. Here, we used high-throughput sequencing of bacterial and fungal ribosomal markers to explore changes in soil microbial community structure under two contrasting tillage regimes (conventional and reduced tillage either with or without crop residue retention. Soil samples were collected over the growing season of two crops (Vicia faba and Triticum aestivum below the seedbed (15–20 cm. Tillage, crop and growing stage were significant determinants of microbial community structure, but the impact of tillage showed only moderate temporal dependency. Whereas the tillage effect on soil bacteria showed some temporal dependency and became less strong at later growing stages, the tillage effect on soil fungi was more consistent over time. Crop residue retention had only a minor influence on the community. Six years after the conversion from conventional to reduced tillage, soil moisture contents and nutrient levels were significantly lower under reduced than under conventional tillage. These changes in edaphic properties were related to specific shifts in microbial community structure. Notably, bacterial groups featuring copiotrophic lifestyles or potentially carrying the ability to degrade more recalcitrant compounds were favored under conventional

Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes.

Science.gov (United States)

Degrune, Florine; Theodorakopoulos, Nicolas; Colinet, Gilles; Hiel, Marie-Pierre; Bodson, Bernard; Taminiau, Bernard; Daube, Georges; Vandenbol, Micheline; Hartmann, Martin

2017-01-01

Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Plowing is a fundamental component of conventional farming, but long-term detrimental effects such as soil erosion and loss of soil organic matter have been recognized. Moving towards more sustainable management practices such as reduced tillage or crop residue retention can reduce these detrimental effects, but will also influence structure and function of the soil microbiota with direct consequences for the associated ecosystem services. Although there is increasing evidence that different tillage regimes alter the soil microbiome, we have a limited understanding of the temporal dynamics of these effects. Here, we used high-throughput sequencing of bacterial and fungal ribosomal markers to explore changes in soil microbial community structure under two contrasting tillage regimes (conventional and reduced tillage) either with or without crop residue retention. Soil samples were collected over the growing season of two crops ( Vicia faba and Triticum aestivum ) below the seedbed (15-20 cm). Tillage, crop and growing stage were significant determinants of microbial community structure, but the impact of tillage showed only moderate temporal dependency. Whereas the tillage effect on soil bacteria showed some temporal dependency and became less strong at later growing stages, the tillage effect on soil fungi was more consistent over time. Crop residue retention had only a minor influence on the community. Six years after the conversion from conventional to reduced tillage, soil moisture contents and nutrient levels were significantly lower under reduced than under conventional tillage. These changes in edaphic properties were related to specific shifts in microbial community structure. Notably, bacterial groups featuring copiotrophic lifestyles or potentially carrying the ability to degrade more recalcitrant compounds were favored under conventional tillage, whereas

Defining Disturbance for Microbial Ecology.

Science.gov (United States)

Plante, Craig J

2017-08-01

Disturbance can profoundly modify the structure of natural communities. However, microbial ecologists' concept of "disturbance" has often deviated from conventional practice. Definitions (or implicit usage) have frequently included climate change and other forms of chronic environmental stress, which contradict the macrobiologist's notion of disturbance as a discrete event that removes biomass. Physical constraints and disparate biological characteristics were compared to ask whether disturbances fundamentally differ in microbial and macroorganismal communities. A definition of "disturbance" for microbial ecologists is proposed that distinguishes from "stress" and other competing terms, and that is in accord with definitions accepted by plant and animal ecologists.

MICROBIAL CELL-SURFACE HYDROPHOBICITY - THE INVOLVEMENT OF ELECTROSTATIC INTERACTIONS IN MICROBIAL ADHESION TO HYDROCARBONS (MATH)

NARCIS (Netherlands)

GEERTSEMADOORNBUSCH, GI; VANDERMEI, HC; BUSSCHER, HJ

Microbial adhesion to hydrocarbons (MATH) is the most commonly used method to determine microbial cell surface hydrophobicity. Since, however, the assay is based on adhesion, it is questionable whether the results reflect only the cell surface hydrophobicity or an interplay of hydrophobicity and

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry.

Science.gov (United States)

Yan, Zaisheng; He, Yuhong; Cai, Haiyuan; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Krumholz, Lee R; Jiang, He-Long

2017-08-01

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

Death and cannibalism in a seasonal environment facilitate bacterial coexistence.

Science.gov (United States)

Rozen, Daniel E; Philippe, Nadège; Arjan de Visser, J; Lenski, Richard E; Schneider, Dominique

2009-01-01

Bacterial populations can evolve and adapt to become diverse niche specialists, even in seemingly homogeneous environments. One source of this diversity arises from newly 'constructed' niches that result from the activities of the bacteria themselves. Ecotypes specialized to exploit these distinct niches can subsequently coexist via frequency-dependent interactions. Here, we describe a novel form of niche construction that is based upon differential death and cannibalism, and which evolved during 20 000 generations of experimental evolution in Escherichia coli in a seasonal environment with alternating growth and starvation. In one of 12 populations, two monophyletic ecotypes, S and L, evolved that stably coexist with one another. When grown and then starved in monoculture, the death rate of S exceeds that of L, whereas the reverse is observed in mixed cultures. As shown by experiments and numerical simulations, the competitive advantage of S cells is increased by extending the period of starvation, and this advantage results from their cannibalization of the debris of lysed L cells, which allows the S cells to increase both their growth rate and total cell density. At the molecular level, the polymorphism is associated with divergence in the activity of the alternative sigma factor RpoS, with S cells displaying no detectable activity, while L cells show increased activity relative to the ancestral genotype. Our results extend the repertoire of known cross-feeding mechanisms in microbes to include cannibalism during starvation, and confirm the central roles for niche construction and seasonality in the maintenance of microbial polymorphisms.

A multiplex, internally controlled real-time PCR assay for detection of toxigenic Clostridium difficile and identification of hypervirulent strain 027/ST-1

DEFF Research Database (Denmark)

Hoegh, A M; Nielsen, J B; Lester, A

2012-01-01

The purpose of this study was to validate a multiplex real-time PCR assay capable of detecting toxigenic Clostridium difficile and simultaneously identifying C. difficile ribotype 027/ST-1 by targeting the toxin genes tcdA, tcdB and cdtA in one reaction and in a separate reaction identifying the Δ...... to confirm the correct identification of the Δ117 deletion in tcdC and C. difficile ribotype 027/ST-1, respectively. The PCR assay displayed a sensitivity, specificity, PPV and NPV of 99.0%, 97.4%, 87.4% and 99.8%, respectively, compared to toxigenic culture on 665 samples evaluable both by PCR and culture....... Sequencing of tcdC, ribotyping and MLST of cultured isolates validated the genotyping assay and confirmed the ability of the assay to correctly identify C. difficile ribotype 027/ST-1 in our current epidemiological setting. We describe the use of a combination of two separate PCR assays for sensitive...

Vitality of aquatic plants and microbial activity of sediment in an oligotrophic lake (Lake Bohinj, Slovenia

Directory of Open Access Journals (Sweden)

Tatjana SIMČIČ

2011-08-01

Full Text Available The vitality of eight macrophyte species and the microbial activity of sediment in an oligotrophic lake (Lake Bohinj, Slovenia were studied via the terminal electron transport system (ETS activity of mitochondria. The levels of ETS activity of vascular plants were as follows: Ranunculus circinatus, Myriohpyllum spicatum, Potamogeton alpinus, P. perfoliatus, P. lucens. Fontinalis antipyretica exhibited the highest ETS activity of the non-vascular plants, followed by charales Chara delicatula and C. aspera. High values enable R. circinatus, an amphibious species with rapid growth, to survive under conditions in which the water level changes throughout the season. M. spicatum, a species with broad ecological tolerance, also exhibited high ETS activity. The ETS activity of the microbial community in sediment was affected by temperature and/or the amount and origin of the organic matter. A positive correlation between the ETS activity of the sediment and that of M. spicatum and R. circinatus was measured, while negative correlations or no correlation were observed for mosses and macroalgae. The high ETS activity in sediment indicates rapid mineralization of organic matter and, in turn, sufficient nutrients for growth of macrophytes.

Influence of moisture content on microbial activity and silage quality during ensilage of food processing residues.

Science.gov (United States)

Zheng, Yi; Yates, Matthew; Aung, Hnin; Cheng, Yu-Shen; Yu, Chaowei; Guo, Hongyun; Zhang, Ruihong; Vandergheynst, Jean; Jenkins, Bryan M

2011-10-01

Seasonally produced biomass such as sugar beet pulp (SBP) and tomato pomace (TP) needs to be stored properly to meet the demand of sustainable biofuel production industries. Ensilage was used to preserve the feedstock. The effect of moisture content (MC) on the performance of ensilage and the relationship between microorganism activities and MC were investigated. For SBP, MC levels investigated were 80, 55, 30, and 10% on a wet basis. For TP, MC levels investigated were 60, 45, 30, and 10%. Organic acids, ethanol, ammonia, pH and water soluble carbohydrates (WSC) were measured to evaluate the silage quality. Ensilage improved as the MC decreased from 80 to 55% for SBP and from 60 to 45% for TP. When the MC decreased to 30%, a little microbial activity was detected for both feedstocks. Storage at 10% MC prevented all the microbial activity. The naturally occurring microorganisms in TP were found to preserve TP during silage and were isolated and determined by polymerase chain reaction (PCR). The results suggest that partial drying followed by ensilage may be a good approach for stabilization of food processing residues for biofuels production.

Post-fire soil functionality and microbial community structure in a Mediterranean shrubland subjected to experimental drought.

Science.gov (United States)

Hinojosa, M Belén; Parra, Antonio; Laudicina, Vito Armando; Moreno, José M

2016-12-15

Fire may cause significant alterations in soil properties. Post-fire soil dynamics can vary depending, among other factors, on rainfall patterns. However, little is known regarding variations in response to post-fire drought. This is relevant in arid and semiarid areas with poor soils, like much of the western Mediterranean. Furthermore, climate change projections in such areas anticipate reduced precipitation and longer annual drought periods, together with an increase in fire severity and frequency. This research evaluates the effects of experimental drought after fire on soil dynamics of a Cistus-Erica shrubland (Central Spain). A replicated (n=4) field experiment was conducted in which the total rainfall and its patterns were manipulated by means of a rain-out shelters and irrigation system. The treatments were: environmental control (natural rainfall), historical control (average rainfall, 2months drought), moderate drought (25% reduction of historical control, 5months drought) and severe drought (45% reduction, 7months drought). After one growing season under these rainfall treatments, the plots were burned. One set of unburned plots under natural rainfall served as an additional control. Soils were collected seasonally. Fire increased soil P and N availability. Post-fire drought treatments reduced available soil P but increased N concentration (mainly nitrate). Fire reduced available K irrespective of drought treatments. Fire reduced enzyme activities and carbon mineralization rate, a reduction that was higher in post-fire drought-treated soils. Fire decreased soil microbial biomass and the proportion of fungi, while that of actinomycetes increased. Post-fire drought decreased soil total microbial biomass and fungi, with bacteria becoming more abundant. Our results support that increasing drought after fire could compromise the resilience of Mediterranean ecosystems to fire. Copyright © 2016 Elsevier B.V. All rights reserved.

Short-term forecasting of non-OPEC supply: a test of seasonality and seasonal decomposition

International Nuclear Information System (INIS)

Jazayeri, S.M.R.T.; Yahyai, A.

2002-01-01

The purpose of this study is, first to find out, based on historical data, whether quarterly averages of non-OPEC supply follow a seasonal pattern. If that is mathematically established, then, secondly, it is attempted to estimate the best seasonal factors to decompose the estimated yearly average into seasonal averages. This study applies the Fourier analysis to quarterly supply series to test for seasonality, and provides estimates of seasonal factors for the year 2001 by applying the so-called X-11 decomposition method to the annual estimate. A set of historical data, consisting of quarterly supply averages of individual countries, regional subtotals and aggregate non-OPEC for the period 1971-2000, forms the basis of the analysis. Through the application of the Fourier analysis and X-11 decomposition method, it is demonstrated that quarterly non-OPEC supply, be it by an individual major producer or regional sub-totals, clearly follows a seasonal pattern. This is a very useful conclusion for the market analyst involved with forecasting the quarterly supply. (author)