18 research outputs found
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 14C-labeled acetate and flow-sorted cells that had been labeled and identified by fluorescence in situ hybridization. Subsequently, scintillography determined the amount of 14C-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 31â62% 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 hostâs reproductive strategy (brooding or broadcast spawning) and reveal previously unknown associations with microbes during lucinid early development
Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions
Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick
mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it
enters the water column. The genus Thiomargarita harbors the largest known freeliving
bacteria with cell sizes of up to 750 mm in diameter. In addition to their ability
to oxidize reduced sulfur compounds, some Thiomargarita spp. are known to store
large amounts of nitrate, phosphate and elemental sulfur internally. To date little is
known about their energy yielding metabolic pathways, and how these pathways
compare to other Beggiatoaceae. Here, we present a draft single-cell genome of a
chain-forming âCandidatus Thiomargarita nelsonii Thio36â, and conduct a comparative
analysis to five draft and one full genome of other members of the Beggiatoaceae. âCa.
T. nelsonii Thio36â is able to respire nitrate to both ammonium and dinitrogen, which
allows them to flexibly respond to environmental changes. Genes for sulfur oxidation
and inorganic carbon fixation confirmed that âCa. T. nelsonii Thio36â can function as
a chemolithoautotroph. Carbon can be fixed via the CalvinâBensonâBassham cycle,
which is common among the Beggiatoaceae. In addition we found key genes of
the reductive tricarboxylic acid cycle that point toward an alternative CO2 fixation
pathway. Surprisingly, âCa. T. nelsonii Thio36â also encodes key genes of the C2-
cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration
in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based
energy bifurcation pathway coupled to a NaC-translocating membrane complex (Rnf).
The coupling of these pathways may be key to surviving long periods of anoxia. As
other Beggiatoaceae âCa. T. nelsonii Thio36â encodes many genes similar to those
of (filamentous) cyanobacteria. In summary, the genome of âCa. T. nelsonii Thio36â
provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals
unique genomic features for the Thiomargarita lineage within the Beggiatoaceae
Distribution of putative denitrifying methane oxidizing bacteria in sediment of a freshwater lake, Lake Biwa
Methane oxidation coupled to denitrification is mediated by 'Candidatus methylomirabilis oxyfera', which belongs to the candidate phylum NC10. The distribution of putative denitrifying methane oxidizing bacteria related to "M. oxyfera" was investigated in a freshwater lake, Lake Biwa, Japan. In the surface layer of the sediment from a profundal site, a phylotype closely related to "M. oxyfera" was most frequently detected among NC10 bacteria in PCR analysis of the 16S rRNA gene. In the sediment, sequences related to "M. oxyfera" were also detected in a pmoA gene library. The presence of NC10 bacteria was also confirmed by catalyzed reporter deposition fluorescence in situ hybridization. Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR indicated that the abundance of "M. oxyfera"-related phylotype was higher in the upper layers of the profundal sediment. The horizontal distribution of the putative methanotrophs in sediment of the lake was also analyzed by DGGE, which revealed that their occurrence was restricted to deep water areas. These results agreed with those in a previous study of another freshwater lake, and suggested that the upper layer of the profundal sediments is major the habitat for denitrifying methanotrophs
Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis
The identity and abundance of potentially active sulfate-reducing bacteria (SRB) in several metre deep sediments of a tidal sand flat in the German Wadden Sea were assessed by directed cultivation and cultivation-independent CARD-FISH analysis (catalysed reporter deposition fluorescence in situ hybridization). Presumably abundant SRB from different sediment layers between 0.5 and 4 m depth were selectively enriched in up to million-fold diluted cultures supplemented with lactate, acetate or hydrogen. Partial 16S rRNA gene sequences obtained from highest dilution steps showing sulfide formation indicated growth of deltaproteobacterial SRB belonging to the Desulfobulbaceae and the Desulfobacteraceae as well as of members of the Firmicutes. Subsequent isolation resulted in 10 novel phylotypes of both litho- and organotrophic sulfate-reducing Deltaproteobacteria. Molecular pre-screening identified six isolates as members of the Desulfobulbaceae, sharing highest identities with either candidatus âDesulfobacterium corrodensâ (95â97%) or Desulfobacterium catecholicum (98%), and four isolates as members of Desulfobacteraceae, being related to either Desulfobacter psychrotolerans (98%) or Desulfobacula phenolica (95â97%). Relatives of D. phenolica were exlusively isolated from 50 and 100 cm deep sediments with 10 and 2 mM of pore water sulfate respectively. In contrast, relatives of D. corrodens, D. psychrotolerans and D. catecholicum were also obtained from layers deeper than 100 cm and with less than 2 mM sulfate. The high in situ abundance of members of both families in sediment layers beneath 50 cm could be confirmed via CARD-FISH analysis performed with a set of six SRB-specific oligonucleotide probes. Moreover, SRB represented a numerically significant fraction of the microbial community throughout the sediment (up to 7%) and reached even higher cell numbers in deep, sulfate-poor layers than in the sulfate-rich surface sediment. This relatively large community size of potentially active SRB in deep sandy sediments might on the one hand be a result of their syntrophic association with other anaerobes. Our results furthermore support the hypothesis that enhanced advective pore water transport might supply nutrients to microbial communities in deep sandy sediments and point to their so far unrecognized contribution to biogeochemical processes in Wadden Sea sediments
Colonization of freshwater bioïŹlms by nitrifying bacteria from activated sludge
12 pĂĄginas, 5 figuras, 2 tablas.Effluents from wastewater treatment plants (WWTPs) containing microorganisms
and residual nitrogen can stimulate nitrification in freshwater
streams. We hypothesized that different ammonia-oxidizing (AOB) and nitriteoxidizing
(NOB) bacteria present in WWTP effluents differ in their potential
to colonize biofilms in the receiving streams. In an experimental approach, we
monitored biofilm colonization by nitrifiers in ammonium- or nitrite-fed
microcosm flumes after inoculation with activated sludge. In a field study, we
compared the nitrifier communities in a full-scale WWTP and in epilithic biofilms
downstream of the WWTP outlet. Despite substantially different ammonia
concentrations in the microcosms and the stream, the same nitrifiers were
detected by fluorescence in situ hybridization in all biofilms. Of the diverse nitrifiers
present in the WWTPs, only AOB of the Nitrosomonas oligotropha/ureae
lineage and NOB of Nitrospira sublineage I colonized the natural biofilms.
Analysis of the amoA gene encoding the alpha subunit of ammonia monooxygenase
of AOB revealed seven identical amoA sequence types. Six of these affiliated
with the N. oligotropha/ureae lineage and were shared between the WWTP
and the stream biofilms, but the other shared sequence type grouped with the
N. europaea/eutropha and N. communis lineage. Measured nitrification activities
were high in the microcosms and the stream. Our results show that nitrifiers
from WWTPs can colonize freshwater biofilms and confirm that WWTPaffected
streams are hot spots of nitrification.This
work was supported by the Austrian Science Fund (FWF)
Grant I44-B06, the Max Planck Society and the European
Science Foundation Contract ERAS-CT-2003-980409 of
the European Commission, DG Research, FP6.Peer reviewe
Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments
Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles
L'influence de l'interventionnisme en politique Ă©conomique sur la diplomatie commerciale: Comparaison de la Wallonie et de la Flandre
Lâobjectif de cette recherche est dâanalyser la diplomatie commerciale de la RĂ©gion wallonne et de la RĂ©gion flamande depuis les annĂ©es 1970. Cette analyse est rĂ©alisĂ©e en utilisant lâhistorico-institutionnalisme pour comprendre comment lâintensitĂ© de la diplomatie commerciale de la RĂ©gion wallonne et la RĂ©gion flamande est diffĂ©rente. Lâeffet de trois variables sur lâintensitĂ© de la diplomatie commerciale est Ă©tudiĂ© : des situations Ă©conomiques diffĂ©rentes dans le passĂ©, la dĂ©pendance au sentier de la politique Ă©conomique et le dynamisme de la politique Ă©conomique.Master [120] en administration publique, UniversitĂ© catholique de Louvain, 201