Dataset Information

Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities.

ABSTRACT: Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity.

SUBMITTER: Lawson CE

PROVIDER: S-EPMC4616946 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities.

Lawson Christopher E CE Strachan Cameron R CR Williams Dominique D DD Koziel Susan S Hallam Steven J SJ Budwill Karen K

Applied and environmental microbiology 20150904 22

Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbi ...[more]

PMID: 26341214

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Project description:Microorganisms mediating ammonia oxidation play a fundamental role in the connection between biological nitrogen fixation and anaerobic nitrogen losses. Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively) have colonized similar habitats worldwide. Ammonia oxidation is the rate-limiting step in nitrification, and the ammonia monooxygenase (Amo) is the key enzyme involved. The molecular ecology of this process has been extensively explored by surveying the gene of the subunit A of the Amo (amoA gene). In the present study, we explored the phylogenetic community ecology of AOB and AOA, analyzing 5776 amoA gene sequences from >300 isolation sources, and clustering habitats by environmental ontologies. As a whole, phylogenetic richness was larger in AOA than in AOB, and sediments contained the highest phylogenetic richness whereas marine plankton the lowest. We also observed that freshwater ammonia oxidizers were phylogenetically richer than their marine counterparts. AOA communities were more dissimilar to each other than those of AOB, and consistent monophyletic lineages were observed for sediments, soils, and marine plankton in AOA but not in AOB. The diversification patterns showed a more constant cladogenesis through time for AOB whereas AOA apparently experienced two fast diversification events separated by a long steady-state episode. The diversification rate (γ statistic) for most of the habitats indicated γ(AOA) > γ(AOB). Soil and sediment experienced earlier bursts of diversification whereas habitats usually eutrophic and rich in ammonium such as wastewater and sludge showed accelerated diversification rates towards the present. Overall, this work shows for the first time a global picture of the phylogenetic community structure of both AOB and AOA assemblages following the strictest analytical standards, and provides an ecological view on the differential evolutionary paths experienced by widespread ammonia-oxidizing microorganisms. The emerged picture of AOB and AOA distribution in different habitats provides a new view to understand the ecophysiology of ammonia oxidizers on Earth.

Project description:BackgroundThe intensification of agricultural practices over the twentieth century led to a cascade of detrimental effects on ecosystems. In Europe, agri-environment schemes (AES) have since been adopted to counter the decrease in farmland biodiversity, with the promotion of extensive habitats such as wildflower strips and extensive meadows. Despite having beneficial effects documented for multiple taxa, their profitability for top farmland predators, like raptors, is still debated. Such species with high movement capabilities have large home ranges with fluctuation in habitat use depending on specific needs.MethodsUsing GPS devices, we recorded positions for 134 barn owls (Tyto alba) breeding in Swiss farmland and distinguished three main behavioural modes with the Expectation-Maximization binary Clustering (EMbC) method: perching, hunting and commuting. We described barn owl habitat use at different levels during the breeding season by combining step and path selection functions. In particular, we examined the association between behavioural modes and habitat type, with special consideration for AES habitat structures.ResultsDespite a preference for the most common habitats at the home range level, behaviour-specific analyses revealed more specific habitat use depending on the behavioural mode. During the day, owls roosted almost exclusively in buildings, while pastures, meadows and forest edges were preferred as nocturnal perching sites. For hunting, barn owls preferentially used AES habitat structures though without neglecting more intensively exploited areas. For commuting, open habitats were preferred over wooded areas.ConclusionsThe behaviour-specific approach used here provides a comprehensive breakdown of barn owl habitat selection during the reproductive season and highlights its importance to understand complex animal habitat preferences. Our results highlight the importance of AES in restoring and maintaining functional trophic chains in farmland.

Dataset Information

Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities.

Publications

Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities.

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