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Cable bacteria are living electric wires, exerting remarkable effects on their surroundings. Despite still refusing pure culture isolation, their biological conductivity and their impact on aquatic sediments give rise to interesting application prospects in environmental and bio-engineering, including bioremediation, the mitigation of greenhouse gas emissions, and bioelectronics. Here, we summarize how research is currently striving to realize the very versatile application potential of these fascinating bacteria. [ABSTRACT FROM AUTHOR]

Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N2 and O2. So far, the ecological role of these microbes is not well understood. The only available tool for a targeted study of oxygenic denitrifiers is their respective maker gene, nitric oxide dismutase (nod). Here, we established the use of PacBio long-read sequencing of nod gene amplicons to study the diversity and community structure of oxygenic denitrifiers. Two distinct sets of environmental samples, agricultural soil and lake sediment, were investigated as examples. The circular consensus sequences (ca 1.0 kb) obtained covered most substitution characteristic of NO dismutase and allowed for reliable classification of oxygenic denitrifiers. Distinct nod gene pools and community structure were revealed for the different habitats, with most sequence types affiliated to yet unidentified environmental nod lineages. The abundance of nod genes ranged 2.2 × 106–3.2 × 107 gene copies g−1 soil or sediment, accounting for up to 3% of total bacterial 16S rRNA gene counts. This study indicates that nod-gene-targeted long-read sequencing can be a powerful tool for studying the ecology of these novel microbes, and the results also suggest that oxygenic denitrifiers are prevalent and abundant in different terrestrial samples, where they could play an important, but yet overlooked role in nitrogen transformations. [ABSTRACT FROM AUTHOR]

Zoogloea oleivorans, capable of using toluene as a sole source of carbon and energy, was earlier found to be an active degrader under microaerobic conditions in aquifer samples. To uncover the genetic background of the ability of microaerobic toluene degradation in Z. oleivorans, the whole-genome sequence of the type strain BucT was revealed. Metatranscriptomic sequence reads, originated from a previous SIP study on microaerobic toluene degradation, were mapped on the genome. The genome (5.68 Mb) had a mean G + C content of 62.5%, 5005 protein coding gene sequences and 80 RNA genes. Annotation predicted that 66 genes were involved in the metabolism of aromatic compounds. Genome analysis revealed the presence of a cluster with genes coding for a multicomponent phenol-hydroxylase system and a complete catechol meta-cleavage pathway. Another cluster flanked by mobile-element protein coding genes coded a partial catechol meta-cleavage pathway including a subfamily I.2.C-type extradiol dioxygenase. Analysis of metatranscriptomic data of a microaerobic toluene-degrading enrichment, containing Z. oleivorans as an active-toluene degrader revealed that a toluene dioxygenase-like enzyme was responsible for the ring-hydroxylation, while enzymes of the partial catechol meta-cleavage pathway coding cluster were responsible for further degradation of the aromatic ring under microaerobic conditions. This further advances our understanding of aromatic hydrocarbon degradation between fully oxic and strictly anoxic conditions. [ABSTRACT FROM AUTHOR]

Background and aims: Forest ecosystems may act as sinks for or source of atmospheric CO. While inorganic nitrogen (N) fertilization increases aboveground tree biomass, the effects on soil and rhizosphere microorganisms are less clear, indicating potentially unpredictable changes in nutrient cycling processes maintaining ecosystem functioning. Although plant-derived carbon (C) is the main C source in soils during the vegetation period, information on the response of rhizosphere bacteria assimilating rhizodeposits to increased soil N availability mainly for trees is missing. Methods: We performed a greenhouse experiment with C-CO labelled young beech seedlings grown under different N fertilization levels. DNA Stable Isotope Probing (DNA-SIP) in combination with TRFLP and pyrosequencing enabled us to identify bacteria assimilating plant-derived C and to assess the main responders phylogenetically. Results: Although above- and belowground allocation of recently fixed photosynthates remained unchanged, microbial rhizosphere community composition was clearly affected by fertilization. Besides, we found lower C incorporation into microbial biomass in fertilized soil. Moreover, it could be shown that only a small subset of the rhizosphere microbiome incorporated recently fixed C into its DNA, dominated by Proteobacteria (Alpha- and Betaproteobacteria) and Actinobacteria (Actinomycetales). Conclusions: Our results suggest that N fertilization may change both the diversity of bacterial communities using rhizodeposits and assimilation rates of recently fixed photosynthates. Given the close interaction of beneficial and/or deleterious microbes and plants in the rhizosphere, this could potentially have positive or negative implications for plant performance on long-term. [ABSTRACT FROM AUTHOR]

Slow sand filtration (SSF) is an effective low-tech water treatment method for pathogen and particle removal. Yet despite its application for centuries, it has been uncertain to which extent pathogenic microbes are removed by mechanical filtration or due to ecological interactions such as grazing and competition for nutrients. In this study, we quantified the removal of bacterial faecal indicators, Escherichia coli and Enterococcus faecalis, from secondary effluent of a wastewater treatment plant and analysed the microbial community composition in compartments of laboratory model SSF columns. The columns were packed with different sand grain sizes and eliminated 1.6-2.3 log units of faecal indicators, which translated into effluents of bathing water quality according to the EU directive (<500 colony forming units of E. coli per 100 ml) for columns with small grain size. Most of that removal occurred in the upper filter area, the Schmutzdecke. Within that same zone, total bacterial numbers increased however, thus suggesting a specific elimination of the faecal indicators. The analysis of the microbial communities also revealed that some taxa were removed more from the wastewater than others. These results accentuate the contribution of biological mechanisms to water purification in SSF. [ABSTRACT FROM AUTHOR]

Biogeochemical and microbiological data indicate that the anaerobic oxidation of non-methane hydrocarbons by sulfate-reducing bacteria (SRB) has an important role in carbon and sulfur cycling at marine seeps. Yet, little is known about the bacterial hydrocarbon degraders active in situ. Here, we provide the link between previous biogeochemical measurements and the cultivation of degraders by direct identification of SRB responsible for butane and dodecane degradation in complex on-site microbiota. Two contrasting seep sediments from Mediterranean Amon mud volcano and Guaymas Basin (Gulf of California) were incubated with 13C-labeled butane or dodecane under sulfate-reducing conditions and analyzed via complementary stable isotope probing (SIP) techniques. Using DNA- and rRNA-SIP, we identified four specialized clades of alkane oxidizers within Desulfobacteraceae to be distinctively active in oxidation of short- and long-chain alkanes. All clades belong to the Desulfosarcina/Desulfococcus (DSS) clade, substantiating the crucial role of these bacteria in anaerobic hydrocarbon degradation at marine seeps. The identification of key enzymes of anaerobic alkane degradation, subsequent β-oxidation and the reverse Wood-Ljungdahl pathway for complete substrate oxidation by protein-SIP further corroborated the importance of the DSS clade and indicated that biochemical pathways, analog to those discovered in the laboratory, are of great relevance for natural settings. The high diversity within identified subclades together with their capability to initiate alkane degradation and growth within days to weeks after substrate amendment suggest an overlooked potential of marine benthic microbiota to react to natural changes in seepage, as well as to massive hydrocarbon input, for example, as encountered during anthropogenic oil spills. [ABSTRACT FROM AUTHOR]

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Global groundwater resources are constantly challenged by a multitude of contaminants such as aromatic hydrocarbons. Especially in anaerobic habitats, a large diversity of unrecognized microbial populations may be responsible for their degradation. Still, our present understanding of the respective microbiota and their ecophysiology is almost exclusively based on a small number of cultured organisms, mostly within the Proteobacteria. Here, by DNA-based stable isotope probing (SIP), we directly identified the most active sulfate-reducing toluene degraders in a diverse sedimentary microbial community originating from a tar-oil-contaminated aquifer at a former coal gasification plant. On incubation of fresh sediments with 13C7-toluene, the production of both sulfide and 13CO2 was clearly coupled to the 13C-labeling of DNA of microbes related to Desulfosporosinus spp. within the Peptococcaceae (Clostridia). The screening of labeled DNA fractions also suggested a novel benzylsuccinate synthase alpha-subunit (bssA) sequence type previously only detected in the environment to be tentatively affiliated with these degraders. However, carbon flow from the contaminant into degrader DNA was only ∼50%, pointing toward high ratios of heterotrophic CO2-fixation during assimilation of acetyl-CoA originating from the contaminant by these degraders. These findings demonstrate that the importance of non-proteobacterial populations in anaerobic aromatics degradation, as well as their specific ecophysiology in the subsurface may still be largely ungrasped. [ABSTRACT FROM AUTHOR]

Here, we present a detailed functional and phylogenetic characterization of an iron-reducing enrichment culture maintained in our lab with benzene as sole carbon and energy source. We used DNA-stable isotope probing to identify microbes within the enrichment most active in the assimilation of 13C-label. When 12C6- and 13C6-benzene were added as comparative substrates, marked differences in the quantitative buoyant density distribution became apparent especially for uncultured microbes within the Gram-positive Peptococcaceae, closely related to environmental clones retrieved from contaminated aquifers world wide and only distantly related to cultured representatives of the genus Thermincola. Prominent among the other constituents of the enrichment were uncultured Deltaproteobacteria, as well as members of the Actinobacteria. Although their presence within the enrichment seems to be stable they did not assimilate 13C-label as significantly as the Clostridia within the time course of our experiment. We hypothesize that benzene degradation in our enrichment involves an unusual syntrophy, where members of the Clostridia primarily oxidize benzene. Electrons from the contaminant are both directly transferred to ferric iron by the primary oxidizers, but also partially shared with the Desulfobulbaceae as syntrophic partners. Alternatively, electrons may also be quantitatively transferred to the partners, which then reduce the ferric iron. Thus our results provide evidence for the importance of a novel clade of Gram-positive iron-reducers in anaerobic benzene degradation, and a role of syntrophic interactions in this process. These findings shed a totally new light on the factors controlling benzene degradation in anaerobic contaminated environments.The ISME Journal (2007) 1, 643–653; doi:10.1038/ismej.2007.73; published online 13 September 2007 [ABSTRACT FROM AUTHOR]

Geothermal energy plays an increasingly important role as a renewable energy source. However, it induces temperature changes in natural thermally static groundwater ecosystems. Temperature impacts can considerably alter the groundwater chemical composition and quality, the metabolism of organisms, and, consequently, biogeochemical processes and ecosystem functions. Combining original data from current studies with a compact review of recent findings, we show that a moderate increase in groundwater/aquifer temperature [+5 to 10 Kelvin (K)] generally causes only minor changes in water chemistry, microbial biodiversity, and ecosystem function in non-contaminated and energy-poor (oligotrophic) groundwater systems. In aquifers that are contaminated with organics, nutrients, and heavy metals—typical in urban areas and at sites with intensive land use (e.g., agriculture)—and particularly at temperatures ≥30 °C as regularly reached when heat is actively stored in aquifers, significant changes in water quality and ecological patterns can result. Here most critical are the heat-related mobilization of organic matter and contaminants (e.g., arsenic), the reduction and depletion of dissolved oxygen, and consequently the consecutive shift to anaerobic redox processes that may produce toxic and corrosive products (e.g., hydrogen sulfide) and greenhouse gases (e.g., methane and carbon dioxide). Severe temperature alterations lead to a reduced biodiversity of the aquifer’s microbial community with the establishment of atypical thermophilic assemblages. Groundwater fauna, which is specifically adapted to the cold groundwater habitat, may be sensitive to thermal changes at temperature increases of only 5 K with long-term emigration or direct lethal effects. From an ecological point of view, long-lasting or reoccurring temperature alterations need to be carefully evaluated and regulated in the future. We suggest developing local and regional vulnerability concepts for the sustainable and ecologically sound use of subterranean heat and cold. [ABSTRACT FROM AUTHOR]