Uncultured Gammaproteobacteria and Desulfobacteraceae Account for Major Acetate Assimilation in a Coastal Marine Sediment

Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Its turnover is central to carbon cycling, however, the relative contribution of different microbial populations to acetate assimilation in marine sediments is unknown. To quantify acetate assimilation by in situ abundant bacterial populations, we incubated coastal marine sediments with C-14-labeled acetate and flow-sorted cells that had been labeled and identified by fluorescence in situ hybridization. Subsequently, scintillography determined the amount of C-14-acetate assimilated by distinct populations. This approach fostered a high-throughput quantification of acetate assimilation by phylogenetically identified populations. Acetate uptake was highest in the oxic-suboxic surface layer for all sorted bacterial populations, including deltaproteobacterial sulfate-reducing bacteria (SRB), which accounted for up to 32% of total bacterial acetate assimilation. We show that the family Desulfobulbaceae also assimilates acetate in marine sediments, while the more abundant Desulfobacteraceae dominated acetate assimilation despite lower uptake rates. Unexpectedly, members of Gammaproteobacteria accounted for the highest relative acetate assimilation in all sediment layers with up to 31-62% of total bacterial acetate uptake. We also show that acetate is used to build up storage compounds such as polyalkanoates. Together, our findings demonstrate that not only the usual suspects SRB but a diverse bacterial community may substantially contribute to acetate assimilation in marine sediments. This study highlights the importance of quantitative approaches to reveal the roles of distinct microbial populations in acetate turnover

Microbial communities in developmental stages of lucinid bivalves

Bivalves from the family Lucinidae host sulfur-oxidizing bacterial symbionts, which are housed inside specialized gill epithelial cells and are assumed to be acquired from the environment. However, little is known about the Lucinidae life cycle and symbiont acquisition in the wild. Some lucinid species broadcast their gametes into the surrounding water column, however, a few have been found to externally brood their offspring by the forming gelatinous egg masses. So far, symbiont transmission has only been investigated in one species that reproduces via broadcast spawning. Here, we show that the lucinid Loripes orbiculatus from the West African coast forms egg masses and these are dominated by diverse members of the Alphaproteobacteria, Clostridia, and Gammaproteobacteria. The microbial communities of the egg masses were distinct from those in the environments surrounding lucinids, indicating that larvae may shape their associated microbiomes. The gill symbiont of the adults was undetectable in the developmental stages, supporting horizontal transmission of the symbiont with environmental symbiont acquisition after hatching from the egg masses. These results demonstrate that L. orbiculatus acquires symbionts from the environment independent of the host’s reproductive strategy (brooding or broadcast spawning) and reveal previously unknown associations with microbes during lucinid early development

Evidence for H-2 consumption by uncultured Desulfobacterales in coastal sediments

Molecular hydrogen (H-2) is the key intermediate in the anaerobic degradation of organic matter. Its removal by H-2-oxidizing microorganisms is essential to keep anaerobic degradation energetically favourable. Sulfate-reducing microorganisms (SRM) are known as the main H-2 scavengers in anoxic marine sediments. Although the community of marine SRM has been extensively studied, those consuming H-2 in situ are completely unknown. We combined metagenomics, PCR-based clone libraries, single-amplified genomes (SAGs) and metatranscriptomics to identify potentially H-2-consuming SRM in anoxic coastal sediments. The vast majority of SRM-related H(2)ase sequences were assigned to group 1b and 1c [NiFe]-H(2)ases of the deltaproteobacterial order Desulfobacterales. Surprisingly, the same sequence types were similarly highly expressed in spring and summer, suggesting that these are stable and integral members of the H-2-consuming community. Notably, one sequence cluster from the SRM group 1 consistently accounted for around half of all [NiFe]-H(2)ase transcripts. Using SAGs, we could link this cluster with the 16S rRNA genes of the uncultured Sva0081-group of the family Desulfobacteraceae. Sequencing of 16S rRNA gene amplicons and H(2)ase gene libraries suggested consistently high in situ abundance of the Sva0081 group also in other marine sediments. Together with other Desulfobacterales these likely are important H-2-scavengers in marine sediments

Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea

The diversity and distribution of Deltaproteobacteria in an intertidal mud flat of the German Wadden Sea was characterized by molecular biological techniques and cultivation. A 16S rRNA gene library generated with general primers (303 clones) suggested that sulfate‐reducing bacteria (SRB) related to Desulfobulbaceae and Desulfosarcina were abundant. Fluorescence in situ hybridization (FISH) with probes targeting these groups was used to characterize their vertical distribution. The combination of FISH with catalysed reporter deposition (CARD–FISH) significantly enhanced the detection of selected subgroups of Deltaproteobacteria, particularly in deeper sediment layers. Up to 11% of all cells were assigned to SRB. Organisms related to Desulfosarcina and Desulfobulbaceae were the dominant SRB in the surface sediments. Two abundant subpopulations of Desulfosarcina‐related bacteria were identified by FISH. The SRB community differed between the sampling site and a sandy intertidal flat chosen as a reference. Enrichments and MPN cultures inoculated with surface sediment were monitored by FISH. Nine strains of Deltaproteobacteria were isolated. Four strains were related to Desulfobulbaceae, such as Desulfobacterium catecholicum and Desulfocapsa spp. A subgroup including clone sequences and strains related to D. catecholicum could be detected in situ by a specific FISH probe. The first physiological experiments suggested specific functional roles for the isolates. Two strains utilized environmentally relevant compounds in coastal areas such as catechol and nitrate. One strain related to Desulfocapsa spp. disproportionated thiosulfate and might thus contribute to the sulfur isotope fractionation at the study site. A Fe(III)‐reducing strain was obtained that affiliated with the Pelobacter–Desulphuromonas group. This group accounted for up to 6% of total cell numbers and even exceeded SRB numbers in upper sediment layers. These bacteria might substantially contribute to carbon mineralization via dissimilatory reduction of, e.g. Fe(III)

Microbial consumption of zero-valence sulfur in marine benthic habitats

Zero-valence sulfur (S-0) is a central intermediate in the marine sulfur cycle and forms conspicuous accumulations at sediment surfaces, hydrothermal vents and in oxygen minimum zones. Diverse microorganisms can utilize S-0, but those consuming S-0 in the environment are largely unknown. We identified possible key players in S-0 turnover on native or introduced S-0 in benthic coastal and deep-sea habitats using the 16S ribosomal RNA approach, (in situ) growth experiments and activity measurements. In all habitats, the epsilonproteobacterial Sulfurimonas/Sulfurovum group accounted for a substantial fraction of the microbial community. Deltaproteobacterial Desulfobulbaceae and Desulfuromonadales were also frequently detected, indicating S-0 disproportionation and S-0 respiration under anoxic conditions. Sulfate production from S-0 particles colonized in situ with Sulfurimonas/Sulfurovum suggested that this group oxidized S-0. We also show that the type strain Sulfurimonas denitrificans is able to access cyclooctasulfur (S-8), a metabolic feature not yet demonstrated for sulfur oxidizers. The ability to oxidize S-0, in particular S-8, likely facilitates niche partitioning among sulfur oxidizers in habitats with intense microbial sulfur cycling such as sulfidic sediment surfaces. Our results underscore the previously overlooked but central role of Sulfurimonas/Sulfurovum group for conversion of free S-0 at the seafloor surface

Influence of temperature, pH, and salinity on membrane lipid composition and TEX 86 of marine planktonic thaumarchaeal isolates

Marine ammonia-oxidizing archaea of the phylum Thaumarchaeota are a cosmopolitan group of microorganisms representing a major fraction of the picoplankton in the ocean. The cytoplasmic membranes of Thaumarchaeota consist predominantly of intact polar isoprenoid glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, which may be used as biomarkers for living Thaumarchaeota. Fossil thaumarchaeal GDGT core lipids accumulate in marine sediments and serve as the basis for geochemical proxies such as the TEX86 paleothermometer. Here, we demonstrate that the responses of membrane lipid compositions and resulting TEX86 values to growth temperature strongly diverge in three closely related thaumarchaeal pure cultures, i.e., Nitrosopumilus maritimus and two novel strains isolated from South Atlantic surface water, although the inventories of intact polar lipids and core lipids were overall similar in the three strains. N. maritimus and its closely related strain NAOA6 showed linear relationships of TEX86 and growth temperature but no correlation of TEX86 and temperature was observed in the more distantly related strain NAOA2. In contrast, the weighted average number of cycloalkyl moieties (ring index) was linearly correlated with growth temperature in all strains. This disparate relationship of TEX86 to growth temperature among closely related Thaumarchaeota suggests that the ring index but not the TEX86 ratio represents a universal response to growth temperature in marine planktonic Thaumarchaeota. Furthermore, the distinct TEX86-temperature relationships in the cultivated strains indicate that environmental GDGT signals may include an ecological component, which has important implications for ocean temperature reconstructions using the TEX86 proxy. In contrast, different growth medium salinities in the range 27–51‰ tested for N. maritimus showed no systematic effect on intact polar GDGT composition and TEX86. Similarly, N. maritimus showed only small changes in intact polar GDGT composition and TEX86 when grown at different medium pH in the range 7.3–7.9. Overall, our pure culture studies suggest that the TEX86 paleotemperature proxy is not solely dependent on growth temperature, but may amalgamate physiological, environmental, and ecological factors

Close association of active nitrifiers with Beggiatoa mats covering deep-sea hydrothermal sediments

Hydrothermal sediments in the Guaymas Basin are covered by microbial mats that are dominated by nitrate-respiring and sulphide-oxidizing Beggiatoa. The presence of these mats strongly correlates with sulphide- and ammonium-rich fluids venting from the subsurface. Because ammonium and oxygen form opposed gradients at the sediment surface, we hypothesized that nitrification is an active process in these Beggiatoa mats. Using biogeochemical and molecular methods, we measured nitrification and determined the diversity and abundance of nitrifiers. Nitrification rates ranged from 74 to 605molNl-1matday-1, which exceeded those previously measured in hydrothermal plumes and other deep-sea habitats. Diversity and abundance analyses of archaeal and bacterial ammonia monooxygenase subunit A genes, archaeal 16S ribosomal RNA pyrotags and fluorescence in situ hybridization confirmed that ammonia- and nitrite-oxidizing microorganisms were associated with Beggiatoa mats. Intriguingly, we observed cells of bacterial and potential thaumarchaeotal ammonia oxidizers attached to narrow, Beggiatoa-like filaments. Such a close spatial coupling of nitrification and nitrate respiration in mats of large sulphur bacteria is novel and may facilitate mat-internal cycling of nitrogen, thereby reducing loss of bioavailable nitrogen in deep-sea sediments