Publications by authors named "Martin Braster"

17 Publications

  • Page 1 of 1

High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers.

Commun Biol 2021 May 5;4(1):530. Epub 2021 May 5.

Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.

A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.
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http://dx.doi.org/10.1038/s42003-021-01948-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099898PMC
May 2021

Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil.

Folia Microbiol (Praha) 2021 Apr 9. Epub 2021 Apr 9.

Systems Biology Lab, Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.

Microbial community profiling using high-throughput sequencing relies in part on the preservation of the DNA and the effectiveness of the DNA extraction method. This study aimed at understanding to what extent these parameters affect the profiling. We obtained samples treated with and without a preservation solution. Also, we compared DNA extraction kits from Qiagen and Zymo-Research. The types of samples were defined strains, both as single species and mixtures, as well as undefined indigenous microbial communities from soil. We show that the use of a preservation solution resulted in substantial changes in the 16S rRNA gene profiles either due to an overrepresentation of Gram-positive bacteria or to an underrepresentation of Gram-negative bacteria. In addition, 16S rRNA gene profiles were substantially different depending on the type of kit that was used for extraction. The kit from Zymo extracted DNA from different types of bacteria in roughly equal amounts. In contrast, the kit from Qiagen preferentially extracted DNA from Gram-negative bacteria while DNA from Gram-positive bacteria was extracted less effectively. These differences in kit performance strongly influenced the interpretation of our microbial ecology studies.
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http://dx.doi.org/10.1007/s12223-021-00866-0DOI Listing
April 2021

Aflatoxins: Occurrence, Exposure, and Binding to Species from the Gut Microbiota of Rural Ugandan Children.

Microorganisms 2020 Feb 29;8(3). Epub 2020 Feb 29.

Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands.

Chronic exposure of children in sub-Saharan Africa to aflatoxins has been associated with low birth weight, stunted growth, immune suppression, and liver function damage. species have been shown to reduce aflatoxin contamination during the process of food fermentation. Twenty-three s strains were isolated from fecal samples obtained from a cohort of rural Ugandan children at the age of 54 to 60 months, typed by 16S rRNA gene sequencing, and characterized in terms of their ability to bind aflatoxin B in vitro. Evidence for chronic exposure of these children to aflatoxin B in the study area was obtained by analysis of local foods (maize flour and peanuts), followed by the identification of the breakdown product aflatoxin M in their urine samples. Surprisingly, in the gut microbiota of 140 children from the same cohort at 24 and 36 months showed the highest positive correlation coefficient with stunting among all bacterial genera identified in the stool samples. This correlation was interpreted to be associated with dietary changes from breastfeeding to plant-based solid foods that pose an additional risk for aflatoxin contamination, on one hand, and lead to increased intake of species on the other.
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http://dx.doi.org/10.3390/microorganisms8030347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143030PMC
February 2020

Long-term exposure of activated sludge in chemostats leads to changes in microbial communities composition and enhanced biodegradation of 4-chloroaniline and N-methylpiperazine.

Chemosphere 2020 Mar 22;242:125102. Epub 2019 Oct 22.

Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.

Exposure history and adaptation of the inoculum to chemicals have been shown to influence the outcome of ready biodegradability tests. However, there is a lack of information about the mechanisms involved in microbial adaptation and the implication thereof for the tests. In the present study, we investigated the impact of a long-term exposure to N-methylpiperazine (NMP) and 4-chloroaniline (4CA) of an activated sludge microbial community using chemostat systems. The objective was to characterize the influence of adaptation to the chemicals on an enhanced biodegradation testing, following the OECD 310 guideline. Cultures were used to inoculate the enhanced biodegradability tests, in batch, before and after exposure to each chemical independently in chemostat culture. Composition and diversity of the microbial communities were characterised by 16s rRNA gene amplicon sequencing. Using freshly sampled activated sludge, NMP was not degraded within the 28 d frame of the test while 4CA was completely eliminated. However, after one month of exposure, the community exposed to NMP was adapted and could completely degrade it. This result was in complete contrast with that from the culture exposed for 3 months to 4CA. Long term incubation in the chemostat system led to a progressive loss of the initial biodegradation capacity of the community, as a consequence of the loss of key degrading microorganisms. This study highlights the potential of chemostat systems to induce adaptation to a specific chemical, ultimately resulting in its biodegradation. At the same time, one should be critical of these observations as the dynamics of a microbial community are difficult to maintain in chemostat, as the loss of 4CA biodegradation capacity demonstrates.
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http://dx.doi.org/10.1016/j.chemosphere.2019.125102DOI Listing
March 2020

Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?

Microorganisms 2019 Aug 8;7(8). Epub 2019 Aug 8.

Department of Molecular Cell Biology, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.

Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we found transfer-persistent arsenite oxidation activity under four conditions (aerobic/anaerobic; heterotrophic/autotrophic). This suggests that biological decontamination may help ameliorate the problem. The enriched microbial communities were phylogenetically at least as diverse as the unenriched communities: they contained a bonanza of 16S rRNA gene sequences. These related to , , , and species. In addition, the enriched microbiomes contained genes highly similar to the arsenite oxidase () gene of chemolithoautotrophic (e.g., sp. SY) and heterotrophic arsenite-oxidizing strains. The enriched cultures also contained phylotypes not detected in the previous survey of uncultivated samples from the same wells. Anaerobic enrichments disclosed a wider diversity of arsenite oxidizing phylotypes than did aerobic enrichments. The cultivatable chemolithoautotrophic and heterotrophic arsenite oxidizers are of great interest for future or arsenic bioremediation technologies for the detoxification of drinking water by oxidizing arsenite to arsenate that should then precipitates with iron oxides. The microbial activities required for such a technology seem present, amplifiable, diverse and hence robust.
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http://dx.doi.org/10.3390/microorganisms7080246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723331PMC
August 2019

Biodegradation of metformin and its transformation product, guanylurea, by natural and exposed microbial communities.

Ecotoxicol Environ Saf 2019 Oct 10;182:109414. Epub 2019 Jul 10.

Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098, XH Amsterdam, the Netherlands.

Metformin (MET) is a pharmaceutical product mostly biotransformed in the environment to a transformation product, guanylurea (GUA). In ready biodegradability tests (RBTs), however, contrasting results have been observed for metformin. The objective of this study was to measure the biodegradation of MET and GUA in RBTs, using activated sludge from the local wastewater treatment plant, either directly or after pre-exposure to MET, in a chemostat. The activated sludge community was cultivated in chemostats, in presence or absence of MET, for a period of nine months, and was used in RBT after one, three and nine months. The results of this study showed that the original activated sludge was able to completely remove MET (15 mg/l) and the newly produced GUA (50% of C) under the test conditions. Inoculation of the chemostat led to a rapid shift in the community composition and abundance. The community exposed to 1.5 mg/l of MET was still able to completely consume MET in the RBTs after one-month exposure, but three- and nine-months exposure resulted in reduced removal of MET in the RBTs. The ability of the activated sludge community to degrade MET and GUA is the result of environmental exposure to these chemicals as well as of conditions that could not be reproduced in the laboratory system. A MET-degrading strain belonging to the genus Aminobacter has been isolated from the chemostat community. This strain was able to completely consume 15 mg/l of MET within three days in the test. However, community analysis revealed that the fluctuation in relative abundance of this genus (<1%) could not be correlated to the fluctuation in biodegradation capacity of the chemostat community.
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http://dx.doi.org/10.1016/j.ecoenv.2019.109414DOI Listing
October 2019

Subsurface landfill leachate contamination affects microbial metabolic potential and gene expression in the Banisveld aquifer.

FEMS Microbiol Ecol 2018 10;94(10)

Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085 HV Amsterdam, the Netherlands.

Microbial communities in groundwater ecosystems can develop the capacity to degrade complex mixtures of chemicals resulting from pollution by landfill leachate. Monitoring this natural attenuation requires insight into the metabolic potential and activity of microbial communities. We contrasted the metagenomes and metatranscriptomes from a leachate-polluted aquifer downstream of the Banisveld (the Netherlands) landfill with uncontaminated groundwater, which revealed changes in microbial genomic content and activity. Banisveld landfill leachate contains mono-aromatic hydrocarbons and the assessment of natural attenuation of these compounds in the aquifer had been a focal point of research. In the contaminated groundwater, active microbial functions were the ones involved in degradation of complex carbon substrates and organic pollutants. We found that benzylsuccinate synthase genes-involved in the catabolism of toluene-were highly expressed close to the source of contamination, confirming the ongoing natural attenuation of organic mono-aromatic hydrocarbon pollution in this aquifer. Additionally, metatranscriptomes were indicative of phosphorus limitation that can constrain total microbial activity and agree with the low phosphate concentrations (<0.4 μmol/L) in this aquifer. Through the application of metagenomics and metatranscriptomics, we were able to determine functional potential and expression patterns to assess the natural attenuation processes and constraints on microbial communities.
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http://dx.doi.org/10.1093/femsec/fiy156DOI Listing
October 2018

Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats.

Environ Microbiol 2018 07;20(7):2652-2669

Molecular Cell Physiology, Faculty of Science, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands.

Desulfitobacterium hafniense Y51 has been widely used in investigations of perchloroethylene (PCE) biodegradation, but limited information exists on its other physiological capabilities. We investigated how D. hafniense Y51 confronts the debilitating limitations of not having enough electron donor (lactate), or electron acceptor (fumarate) during cultivation in chemostats. The residual concentrations of the substrates supplied in excess were much lower than expected. Transcriptomics, proteomics and fluxomics were integrated to investigate how this phenomenon was regulated. Through diverse regulation at both transcriptional and translational levels, strain Y51 turned to fermenting the excess lactate and disproportionating the excess fumarate under fumarate- and lactate-limiting conditions respectively. Genes and proteins related to the utilization of a variety of alternative electron donors and acceptors absent from the medium were induced, apparently involving the Wood-Ljungdahl pathway. Through this metabolic flexibility, D. hafniense Y51 may be able to switch between different metabolic capabilities under limiting conditions.
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http://dx.doi.org/10.1111/1462-2920.14295DOI Listing
July 2018

The influence of long-term copper contaminated agricultural soil at different pH levels on microbial communities and springtail transcriptional regulation.

Environ Sci Technol 2012 Jan 16;46(1):60-8. Epub 2011 Sep 16.

Department of Ecological Sciences, VU University, de Boelelaan 1085, 1081HV, Amsterdam, The Netherlands.

Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail Folsomia candida an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology.
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http://dx.doi.org/10.1021/es2013598DOI Listing
January 2012

Molecular diversity and distribution of aromatic hydrocarbon-degrading anaerobes across a landfill leachate plume.

Environ Microbiol 2011 May 31;13(5):1216-27. Epub 2011 Jan 31.

Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands.

Natural attenuation of the mono-aromates benzene, toluene, ethylbenzene and xylene occurs under iron-reducing conditions in a leachate-contaminated aquifer near the Banisveld landfill, the Netherlands. The diversity of mono-aromate-degrading microorganisms was studied by targeting functional genes encoding benzylsuccinate synthase α-subunit (bssA) and 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase (bamA). Sixty-four bssA and 188 bamA variants were sequenced from groundwater sampled along the pollution plume in 1999 and 2004. Species containing bssA sequences closest affiliated (> 91%) with the betaprotebacterium Georgfuchsia toluolica were the dominant alkylbenzene degraders (89% of bssA sequences). bssA genes were found at more than 10-fold lower copy numbers than bamA genes, of which only a small fraction (< 2%) was closely related to the genes of Georgfuchsia. bamA gene diversity was high and bamA-based community composition was primarily affected by dissolved organic carbon (DOC) and ferrous iron concentrations. bamA sequences closest related to Geobacteraceae were dominantly (43.2%) observed and the presence of Geobacteraceae-related bamA sequences was associated with DOC. Our results indicate a key role for specialized Georgfuchsia spp. in the degradation of alkylbenzenes, whereas Geobacteraceae are involved in degradation of aromatics other than toluene and xylene.
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http://dx.doi.org/10.1111/j.1462-2920.2010.02421.xDOI Listing
May 2011

Spatial heterogeneity in sediment-associated bacterial and eukaryotic communities in a landfill leachate-contaminated aquifer.

FEMS Microbiol Ecol 2008 Sep 8;65(3):534-43. Epub 2008 Jul 8.

Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands.

Heterogeneity in eukaryotic and bacteria community structure in surface and subsurface sediment samples downgradient of the Banisveld landfill (The Netherlands) was studied using a culturing-independent molecular approach. Along a transect covering the part of the aquifer most polluted by landfill leachate, sediment was sampled at 1-m depth intervals, until a depth of 5.5 m, at four distances from the landfill. Two drillings were placed in a nearby clean area as a reference. Denaturing gradient gel electrophoresis banding patterns revealed high bacterial and eukaryotic diversity and complex community structures. Bacteria and eukaryotic community profiles in polluted samples grouped different from those in clean samples. Bacteria community profiles in surface samples clustered together and separately from subsurface community profiles. Subsurface bacteria profiles clustered in a location-specific manner. Eukaryotic community structure did not significantly relate to distance from the landfill or depth. No significant spatial autocorrelation of bacteria or eukaryotic communities was observed over 1-m depth intervals per sampling location. Spatial heterogeneity in sediment-associated bacterial communities appears to be much larger than in groundwater. We discuss how on the one hand, spatial heterogeneity may complicate the assessment of microbial community structure and functioning, while on the other it may provide better opportunities for natural attenuation.
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http://dx.doi.org/10.1111/j.1574-6941.2008.00533.xDOI Listing
September 2008

Eukaryotic diversity in an anaerobic aquifer polluted with landfill leachate.

Appl Environ Microbiol 2008 Jul 9;74(13):3959-68. Epub 2008 May 9.

Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands.

Eukaryotes may influence pollutant degradation processes in groundwater ecosystems by activities such as predation on bacteria and recycling of nutrients. Culture-independent community profiling and phylogenetic analysis of 18S rRNA gene fragments, as well as culturing, were employed to obtain insight into the sediment-associated eukaryotic community composition in an anaerobic sandy aquifer polluted with landfill leachate (Banisveld, The Netherlands). The microeukaryotic community at a depth of 1 to 5 m below the surface along a transect downgradient (21 to 68 m) from the landfill and at a clean reference location was diverse. Fungal sequences dominated most clone libraries. The fungal diversity was high, and most sequences were sequences of yeasts of the Basidiomycota. Sequences of green algae (Chlorophyta) were detected in parts of the aquifer close (<30 m) to the landfill. The bacterium-predating nanoflagellate Heteromita globosa (Cercozoa) was retrieved in enrichments, and its sequences dominated the clone library derived from the polluted aquifer at a depth of 5 m at a location 21 m downgradient from the landfill. The number of culturable eukaryotes ranged from 10(2) to 10(3) cells/g sediment. Culture-independent quantification revealed slightly higher numbers. Groundwater mesofauna was not detected. We concluded that the food chain in this polluted aquifer is short and consists of prokaryotes and fungi as decomposers of organic matter and protists as primary consumers of the prokaryotes.
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http://dx.doi.org/10.1128/AEM.02820-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2446530PMC
July 2008

Dominance of Geobacteraceae in BTX-degrading enrichments from an iron-reducing aquifer.

FEMS Microbiol Ecol 2007 Oct 3;62(1):118-30. Epub 2007 Sep 3.

Earth Surface Processes and Materials Department, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.

Microbial community structure was linked to degradation potential in benzene-, toluene- or xylene- (BTX) degrading, iron-reducing enrichments derived from an iron-reducing aquifer polluted with landfill leachate. Enrichments were characterized using 16S rRNA gene-based analysis, targeting of the benzylsuccinate synthase-encoding bssA gene and phospholipid fatty acid (PLFA) profiling in combination with tracking of labelled substrate. 16S rRNA gene analysis indicated the dominance of Geobacteraceae, and one phylotype in particular, in all enrichments inoculated with polluted aquifer material. Upon cultivation, progressively higher degradation rates with a concomitant decrease in species richness occurred in all primary incubations and successive enrichments. Yet, the same Geobacteraceae phylotype remained common and dominant, indicating its involvement in BTX degradation. However, the bssA gene sequences in BTX degrading enrichments differed considerably from those of Geobacter isolates, suggesting that the first steps of toluene, but also benzene and xylene oxidation, are carried out by another member of the enrichments. Therefore, BTX would be synthrophically degraded by a bacterial consortium in which Geobacteraceae utilized intermediate metabolites. PLFA analysis in combination with (13)C-toluene indicated that the enriched Geobacteraceae were assimilating carbon originally present in toluene. Combined with previous studies, this research suggests that Geobacteraceae play a key role in the natural attenuation of each BTX compound in situ.
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http://dx.doi.org/10.1111/j.1574-6941.2007.00371.xDOI Listing
October 2007

Phylogenetic and physiological diversity of dissimilatory ferric iron reducers in sediments of the polluted Scheldt estuary, Northwest Europe.

Environ Microbiol 2007 Aug;9(8):1956-68

Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.

The potential for dissimilatory ferric iron [Fe(III)] reduction in intertidal sediments of the polluted Scheldt estuary, Northwest Europe, was assessed by combining field-based geochemical measurements with laboratory experiments on the associated microbiology. Microbial communities at a freshwater and brackish location were characterized by culture-independent 16S rRNA gene analysis, as well as enrichments, strain isolation and physiological screening. Dilution-to-extinction batch enrichments using a variety of Fe(III) sources were performed. The dilution factor of the inoculum in the enrichments had a more determining effect on the Fe(III)-reducing microbial community structure than the Fe(III) source. Well-known Fe(III) reducers, including members of the family Geobacteraceae and the genus Shewanella, constituted only a small fraction (< or = 1%) of the in situ microbial community. Instead, facultative anaerobic Ralstonia and strictly anaerobic, spore-forming Clostridium species dominated Fe(III) reduction. These species were able to utilize a variety of electron acceptors. This flexibility may help the organisms to survive in the dynamic estuarine environment. The high diversity and abundance of culturable Fe(III) reducers (4.6 x 10(5) and 2.4 x 10(4) cells g(-1) sediment at the freshwater and brackish site respectively), plus the high concentrations of chemically reducible solid-phase Fe(III) at the sites, implied a high potential for dissimilatory Fe(III) reduction in the estuarine sediments. Pore water chemical data further supported in situ dissimilatory Fe(III) reduction.
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http://dx.doi.org/10.1111/j.1462-2920.2007.01312.xDOI Listing
August 2007

Microbial communities in the world's largest acidic volcanic lake, Kawah Ijen in Indonesia, and in the Banyupahit river originating from it.

Microb Ecol 2006 Nov 11;52(4):609-18. Epub 2006 Oct 11.

Department of Animal Ecology, Institute of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.

A first study was made on the microbial community composition of the Indonesian crater lake Kawah Ijen (pH < 0.3) and the Banyupahit-Banyuputih river (pH 0.4-3.5) originating from it. Culture-independent, rRNA gene-based denaturing gradient gel electrophoresis was used to profile microbial communities in this natural and ancient, extremely acidic environment. Similarity in community profiles of the different sampling locations was low, indicating heterogeneity in community composition. Archaea were present at all sampling locations; archaeal diversity was low at the most acidic locations and increased at pH >2.6. Bacteria were not detected in the water column of the crater lake, but were found at all locations along the acidic river. Bacterial diversity increased with increasing pH. Eukarya were only present at pH >2.6. Retrieved rRNA gene sequences of Bacteria and Archaea were not closely related to known acidophilic species. It is concluded that tolerance to extreme acidity in this system is developed most extensively among Archaea. The acidity gradient of the Banyupahit-Banyuputih river has a clear effect on microbial community composition and biodiversity.
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http://dx.doi.org/10.1007/s00248-006-9068-2DOI Listing
November 2006

Geobacteraceae community composition is related to hydrochemistry and biodegradation in an iron-reducing aquifer polluted by a neighboring landfill.

Appl Environ Microbiol 2005 Oct;71(10):5983-91

Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, NL-1081 HV Amsterdam, The Netherlands.

Relationships between community composition of the iron-reducing Geobacteraceae, pollution levels, and the occurrence of biodegradation were established for an iron-reducing aquifer polluted with landfill leachate by using cultivation-independent Geobacteraceae 16S rRNA gene-targeting techniques. Numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles and sequencing revealed a high Geobacteraceae diversity and showed that community composition within the leachate plume differed considerably from that of the unpolluted aquifer. This suggests that pollution has selected for specific species out of a large pool of Geobacteraceae. DGGE profiles of polluted groundwater taken near the landfill (6- to 39-m distance) clustered together. DGGE profiles from less-polluted groundwater taken further downstream did not fall in the same cluster. Several individual DGGE bands were indicative of either the redox process or the level of pollution. This included a pollution-indicative band that dominated the DGGE profiles from groundwater samples taken close to the landfill (6 to 39 m distance). The clustering of these profiles and the dominance by a single DGGE band corresponded to the part of the aquifer where organic micropollutants and reactive dissolved organic matter were attenuated at relatively high rates.
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http://dx.doi.org/10.1128/AEM.71.10.5983-5991.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1266018PMC
October 2005

Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java, Indonesia.

Environ Microbiol 2002 Jun;4(6):361-73

Section Molecular Microbial Ecology, Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, Research School SENSE, Vrije Universiteit, De Boelelaan 1087, NL-1081 HV Amsterdam, The Netherlands.

In Java, Indonesia, many nutrient-poor soils are intensively reforested with Pinus merkusii (pine). Information on nutrient cycles and microorganisms involved in these cycles will benefit the management of these important forests. Here, seasonal effects on the stratification of bacterial community structure in the soil profile of a tropical pine forest are described, and differences in bacterial communities are related to chemical and physical soil parameters. Culture-independent community profiles of litter, fragmented litter and mineral soil layers were made by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA-specific polymerase chain reaction (PCR) fragments. The community profiles of the different soil layers clustered separately, correlating with significant differences in organic matter content between the three layers. The bacterial communities appeared to be stable during the wet season of 1998. The drought in 1997, caused by the El Niño climatic effect, did not influence the bacterial communities in fragmentation and mineral soil, although moisture content and other soil parameters were markedly lower than in the wet season. However, communities in litter were influenced by drought. In the litter layer, the moisture content was significantly lower than in the fragmentation and mineral layers during the dry season. A clone library was made from a litter sample taken during the wet season. Partial sequencing of 74 clones and linking the DGGE banding positions of these clones to bands in the DGGE profile of the sample from which the clone library was derived showed considerable bacterial diversity. Alpha-proteobacteria (40.5% of the clones, of which 57% belonged to the Rhizobium-Agrobacterium group) and high-G+C content, Gram-positive bacteria (36.5%) dominated the clone library.
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http://dx.doi.org/10.1046/j.1462-2920.2002.00304.xDOI Listing
June 2002