Under anoxic conditions in sediments, acetogens are often thought to be outcompeted by microorganisms performing energetically more favorable metabolic pathways, such as sulfate reduction or ...methanogenesis. Recent evidence from deep subseafloor sediments suggesting acetogenesis in the presence of sulfate reduction and methanogenesis has called this notion into question, however. Here I argue that acetogens can successfully coexist with sulfate reducers and methanogens for multiple reasons. These include (1) substantial energy yields from most acetogenesis reactions across the wide range of conditions encountered in the subseafloor, (2) wide substrate spectra that enable niche differentiation by use of different substrates and/or pooling of energy from a broad range of energy substrates, (3) reduced energetic cost of biosynthesis among acetogens due to use of the reductive acetyl CoA pathway for both energy production and biosynthesis coupled with the ability to use many organic precursors to produce the key intermediate acetyl CoA. This leads to the general conclusion that, beside Gibbs free energy yields, variables such as metabolic strategy and energetic cost of biosynthesis need to be taken into account to understand microbial survival in the energy-depleted deep biosphere.
In marine sediments, DNA occurs both inside and outside living organisms. DNA not enclosed in living cells may account for the largest fraction of total DNA, and include molecules locked within dead ...cells, organic and inorganic aggregates, adsorbed onto mineral matrices, and viral DNA. This DNA comprises genetic material released in situ from sediment microbial communities, as well as DNA of pelagic and terrestrial origin deposited to the seafloor. DNA not enclosed in living cells undermines the assumption of a direct link between the overall DNA pool and the local, currently living microbial assemblages, in terms of both microbial cell abundance and diversity. At the same time, the extracellular DNA may provide an integrated view of the biodiversity and ecological processes occurring on land, in marine water columns, and sediments themselves, thereby acting as an archive of genetic information which can be used to reconstruct past changes in source environments. In this review, we identify and discuss DNA pools in marine sediments, with special focus on DNA not enclosed in living cells, its origin, dynamics, and ecological and methodological implications. Achievements in deciphering the genetic information held within each DNA pool are presented along with still-standing challenges and major gaps in current knowledge.
The factors controlling the relative abundances of Archaea and Bacteria in marine sediments are poorly understood. We determined depth distributions of archaeal and bacterial 16S rRNA genes by ...quantitative PCR at eight stations in Aarhus Bay, Denmark. Bacterial outnumber archaeal genes 10-60-fold in uppermost sediments that are irrigated and mixed by macrofauna. This bioturbation is indicated by visual observations of sediment color and faunal tracks, by porewater profiles of dissolved inorganic carbon and sulfate, and by distributions of unsupported
Pb and
Cs. Below the depth of bioturbation, the relative abundances of archaeal genes increase, accounting for one third of 16S rRNA genes in the sulfate zone, and half of 16S rRNA genes in the sulfate-methane transition zone and methane zone. Phylogenetic analyses reveal a strong shift in bacterial and archaeal community structure from bioturbated sediments to underlying layers. Stable isotopic analyses on organic matter and porewater geochemical gradients suggest that macrofauna mediate bacterial dominance and affect microbial community structure in bioturbated sediment by introducing fresh organic matter and high-energy electron acceptors from overlying seawater. Below the zone of bioturbation, organic matter content and the presence of sulfate exert key influences on bacterial and archaeal abundances and overall microbial community structure.
A New Era of Methanogenesis Research Lever, Mark Alexander
Trends in microbiology (Regular ed.),
02/2016, Letnik:
24, Številka:
2
Journal Article
Recenzirano
The reductive acetyl-CoA pathway coupled to methanogenesis is likely one of Earth's oldest metabolisms. Yet, until recently this metabolism had only been found in the kingdom Euryarchaeota. A study ...now suggests that distantly related Bathyarchaeota are also methanogens and that methane metabolism is more phylogenetically widespread than previously thought.
The accuracy of flow cytometric (FCM) quantifications of microbial populations in sediments varies with FCM settings, cell extraction and staining protocols, as well as sample types. In the present ...study, we improve the accuracy of FCM for enumerating microorganisms inhabiting diverse lake and marine sediment types based on extensive tests with FCM settings, extraction buffer chemical compositions, cell separation methods, and staining procedures. Tests on the FCM settings, (e.g., acquisition time, rates of events) and salinity of extraction solutions show minor impacts on FCM enumerations and yields of cell extraction, respectively. Existing methods involving hydrofluoric acid (HF) treatment to release sediment-attached cells into solution prove effective on both marine and freshwater samples. Yet, different staining techniques (direct staining of cell extracts, staining of membrane-filtered cell extracts) produce clear differences in cell number estimates. We demonstrate that, while labor-intensive membrane-staining generates high cell staining efficiency and accurate cell counts that are consistent across FCM and epifluorescence microscopy-based (EFM) quantification methods, accurate cell counts determined by more time- and labor-efficient direct staining require consideration of dye concentration, sample dilution, and lithology. Yet, good agreement between the two staining methods can be achieved through sample-specific adjustments of dye concentrations and sample dilutions during direct staining. We thus present a complete protocol for FCM-based cell quantification, that includes all steps from the initial sample fixation to the final enumeration, with recommendations for buffer compositions, direct and membrane-based staining procedures, and the final FCM assay. This protocol is versatile, accurate, and reliable, as is evident from good agreement with cell quantifications by EFM and quantitative polymerase chain reaction (qPCR) of 16S rRNA genes across a wide range of sedimentary sample types.
Even though sediment macrofauna are widespread in the global seafloor, the influence of these fauna on microbial communities that drive sediment biogeochemical cycles remains poorly understood. ...According to recent field investigations, macrofaunal activities control bacterial and archaeal community structure in surface sediments, but the inferred mechanisms have not been experimentally verified. Here we use laboratory microcosms to investigate how activities of two major polychaete guilds, the lugworms, represented by
Abarenicola pacifica
, and the clamworms, represented by
Nereis vexillosa
, influence microbial communities in coastal sediments.
A. pacifica
treatments show >tenfold increases in microbial cell-specific consumption rates of oxygen and nitrate, largely due to the strong ventilation activity of
A. pacifica
. While ventilation resulted in clearly elevated percentages of nitrifying archaea (
Nitrosopumilus
spp.) in surface sediments, it only minorly affected bacterial community composition. By comparison, reworking – mainly by deposit-feeding of
A. pacifica
– had a more pronounced impact on microorganismal communities, significantly driving down abundances of Bacteria and Archaea. Within the Bacteria, lineages that have been linked to the degradation of microalgal biomass (e.g., Flavobacteriaceae and Rhodobacteraceae), were especially affected, consistent with the previously reported selective feeding of
A. pacifica
on microalgal detritus. In contrast,
N. vexillosa
, which is not a deposit feeder, did not significantly influence microbial abundances or microbial community structure. This species also only had a relatively minor impact on rates of oxygen and nitrogen cycling, presumably because porewater exchanges during burrow ventilation by this species were mainly restricted to sediments immediately surrounding the burrows. Collectively our analyses demonstrate that macrofauna with distinct bioturbation modes differ greatly in their impacts on microbial community structure and microbial metabolism in marine sediments.
Serpentinitic systems are potential habitats for microbial life due to frequently high concentrations of microbial energy substrates, such as hydrogen (H
), methane (CH
), and short-chain organic ...acids (SCOAs). Yet, many serpentinitic systems are also physiologically challenging environments due to highly alkaline conditions (pH > 10) and elevated temperatures (>80°C). To elucidate the possibility of microbial life in deep serpentinitic crustal environments, International Ocean Discovery Program (IODP) Expedition 366 drilled into the Yinazao, Fantangisña, and Asùt Tesoru serpentinite mud volcanoes on the Mariana Forearc. These mud volcanoes differ in temperature (80, 150, 250°C, respectively) of the underlying subducting slab, and in the porewater pH (11.0, 11.2, 12.5, respectively) of the serpentinite mud. Increases in formate and acetate concentrations across the three mud volcanoes, which are positively correlated with temperature in the subducting slab and coincide with strong increases in H
concentrations, indicate a serpentinization-related origin. Thermodynamic calculations suggest that formate is produced by equilibrium reactions with dissolved inorganic carbon (DIC) + H
, and that equilibration continues during fluid ascent at temperatures below 80°C. By contrast, the mechanism(s) of acetate production are not clear. Besides formate, acetate, and H
data, we present concentrations of other SCOAs, methane, carbon monoxide, and sulfate, δ
C-data on bulk carbon pools, and microbial cell counts. Even though calculations indicate a wide range of microbial catabolic reactions to be thermodynamically favorable, concentration profiles of potential energy substrates, and very low cell numbers suggest that microbial life is scarce or absent. We discuss the potential roles of temperature, pH, pressure, and dispersal in limiting the occurrence of microbial life in deep serpentinitic environments.
A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields ...in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world's oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample types and research goals.
Stable isotope probing (SIP) of deoxyribonucleic acid (DNA) was used to identify microbes incorporating ¹³C‐labeled acetate in sulfate‐reducing sediment from Aarhus Bay, Denmark. Sediment was ...incubated in medium containing 10 mM sulfate and different ¹³C‐acetate (10, 1, 0.1 mM) concentrations. The resultant changes in microbial community composition were monitored in total and SIP‐fractionated DNA during long‐term incubations. Chemical analyses demonstrated metabolic activity in all sediment slurries, with sulfate‐reducing activity largely determined by initial acetate concentrations. Sequencing of 16S rRNA gene PCR amplicons showed that the incubations shifted the bacterial but not the archaeal community composition. After 3 months of incubation, only sediment slurries incubated with 10 mM ¹³C‐acetate showed detectable ¹³C‐DNA labeling. Based on 16S rRNA and dsrB gene PCR amplicon sequencing, the ¹³C‐labeled DNA pool was dominated by a single type of sulfate reducer representing a novel genus in the family Desulfobacteraceae. In addition, members of the uncultivated Crenarchaeotal group C3 were enriched in the ¹³C‐labeled DNA. Our results were reproducible across biological replicate experiments and provide new information about the identities of uncultured acetate‐consuming bacteria and archaea in marine sediments.
Macroinvertebrates are widespread in lake sediments and alter sedimentary properties through their activity (bioturbation). Understanding the interactions between bioturbation and sediment properties ...is important given that lakes are important sinks and sources of carbon and nutrients. We studied the biogeochemical impact of macrofauna on surface sediments in 3-month-long mesocosm experiments conducted using sediment cores from a hypoxic, macrofauna-free lake basin. Experimental units consisted of hypoxic controls, oxic treatments, and oxic treatments that were experimentally colonized with chironomid larvae or tubificid worms. Overall, the presence of O2 in bottom water had the strongest geochemical effect and led to oxidation of sediments down to 2 cm depth. Relative to macrofauna-free oxic treatments, chironomid larvae increased sediment pore water concentrations of nitrate and sulfate and lowered porewater concentrations of reduced metals (Fe2+, Mn2+), presumably by burrow ventilation, whereas tubificid worms increased the redox potential, possibly through sediment reworking. Microbial communities were very similar across oxic treatments; however, the fractions of α-, β-, and γ-Proteobacteria and Sphingobacteriia increased, whereas those of Actinobacteria, Planctomycetes, and Omnitrophica decreased compared to hypoxic controls. Sediment microbial communities were, moreover, distinct from those of macrofaunal tubes or feces. We suggest that, under the conditions studied, bottom water oxygenation has a stronger biogeochemical impact on lacustrine surface sediments than macrofaunal bioturbation.
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