Bacterial diversity in deep-sea sediments from different depths (original) (raw)
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Deep Sea Research Part I: Oceanographic Research Papers, 2013
The relationship between surface-derived particulate organic matter (POM) and deep-sea sediment bacterial abundance, community structure and composition was investigated in two different sediment layers from two zones of contrasting surface water productivity in the southern Indian Ocean. Bacterial sediment communities from high chlorophyll (HC) and low chlorophyll (LC) sites were characterized and compared using direct counts, clone library construction, denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH). Of the 1566 bacterial clones generated from the sediment communities, 1010 matched published 16S rDNA sequences at 97% identity. A comparison of surface sediment clone libraries showed that at least one third of all identified operational taxonomic units (OTUs) were common to both HC and LC sites. DGGE community profiles were consistent (82% similar) and evenness of the major phylogenetic groups was 96% similar between surface sediment communities, where gamma-and alpha-Proteobacteria were dominant. Sediment communities shared similarly high biodiversity, while species richness was marginally higher at the LC site. Intra-site shifts in bacterial abundance and composition were observed with increasing sediment depth. Despite the differences in organic matter input between sites, the consistency observed between HC and LC sediment communities pointed to 1) the extent of remineralisation by mega and meio-fauna was a factor affecting the quantity and quality of POM available to sediment bacteria, 2) sampling during the early 'nutrient assimilation phase' of the bacterial response to freshly deposited POM or 3) the action of bacteria in the water column could affect the quantity and quality of POM available to sediment bacteria. Although factors other than these may explain the observed similarities, this first comparison of deep-sea sediment communities in relation to surface-derived productivity may be useful in further elucidating the role of sediment bacteria in carbon remineralisation in the deep-sea environment.
Sediment Bacterial Communities Reflect the History of a Sea Basin
PLoS ONE, 2013
How entire microbial communities are structured across stratified sediments from the historical standpoint is unknown. The Baltic Sea is an ideal research object for historical reconstruction, since it has experienced many fresh-and brackish water periods and is depleted of dissolved oxygen, which increases the sediment's preservation potential. We investigated the bacterial communities, chemical elements (e.g. Cr, Pb Na, P, Sr and U) and sediment composition in a stratified sediment core dated by radiocarbon and spanning 8000 years of Baltic Sea history, using up-to-date multivariate statistics. The communities were analysed by 16S rRNA gene terminal restriction fragment length polymorphism. The communities of the deep Early Litorina and surface Late Litorina Sea laminae were separated from the communities of the middle Litorina Sea laminae, which were associated with elevated concentrations of U and Sr trace elements, palaeo-oxygen and palaeosalinity proxies. Thus, the Litorina Sea laminae were characterized by past oxygen deficiency and salinity increase. The communities of the laminae, bioturbated and homogeneous sediments were differentiated, based on the same historical sea phases, with correct classifications of 90%. Palaeosalinity was one of the major parameters that separated the bacterial communities of the stratified sediments. A discontinuous spatial structure with a surprising increase in community heterogeneity was detected in Litorina Sea sediments from 388 to 422 cm deep, which suggests that a salinity maximum occurred in the central Gulf of Finland app. 6200-6600 years ago. The community heterogeneity decreased from the surface down to 306 cm, which reflected downcore mineralization. The plateau of the decrease was in the app. 2000-year-old sediment layers. Bacterial community data may be used as an additional tool in ocean-drilling projects, in which it is important to detect mineralization plateaus both to determine historically comparable portions of sediment samples and historical events, such as sea-level rise culminations. Citation: Lyra C, Sinkko H, Rantanen M, Paulin L, Kotilainen A (2013) Sediment Bacterial Communities Reflect the History of a Sea Basin. PLoS ONE 8(1): e54326.
The investigated deeply buried marine sediments of the shallow shelf off New Jersey, USA, are characterized by low organic carbon content and total cell counts of < 10 7 cells per mL sediment. The qPCR data for Bacteria and Archaea were in the same orders of magnitude as the total cell counts. Archaea and Bacteria occurred in similar 16S rRNA gene copy numbers in the upper part of the sediments, but Bacteria dominated in the lowermost part of the analyzed sediment cores down to a maximum analyzed depth of c. 50 meters below seafloor (mbsf). The bacterial candidate division JS1 and the classes Anaerolineae and Caldinilineae of the Chloroflexi were almost as highly abundant as the total Bacteria. Similarly high dsrA gene copy numbers were found for sulfate reducers. The abundance of the Fe(III) and Mn(IV) reducers comprising Geobacteraceae in the upper c. 15 mbsf correlated with concentrations of manganese and iron in the pore water. The isolated 16S rRNA gene sequences of Archaea in clone libraries could be allocated to the phyla Thaumarchaeota, Euryarchaeota, and Crenarchaeota with 1%, 14%, and 85%, respectively. The typical deep subsurface sediment-associated groups MBG-B, MBG-D, MCG, and SAGMEG were represented in the sediment community. MCG was the dominant group with a high diversity of the isolated 16S rRNA gene sequences.
Microbial Ecol, 2005
16S rRNA gene-based molecular analyses revealed the presence of several large and so far uncultivated clades within class c-Proteobacteria, designated c-proteobacterial marine sediment (GMS) clades 1 to 4, in marine sediment. The GMS clades appear only indigenous to marine sediment and so far have an unknown functionality. SYBR Green-based real-time PCR analyses using GMS clade-specific primers indicated GMS clades were a significant part of the bacterial community (0.3-8.7% of total 16S rRNA genes) in both polar and temperate marine sediment samples. Univariate statistical analyses indicated that GMS clade communities were indistinguishable in two temperate coastal sediment samples even though these possessed very different mean grain sizes, organic contents, and organic loading rates. GMS clade communities were slightly different (p < 0.05) between polar and temperate sites, suggesting that psychrophilic adaptation among GMS clade taxa corresponds only to subtle phylogenetic differences. Similar levels of difference were also observed through a sediment core reflecting that through the sediment core history, which spanned 3000 years, GMS clonal diversity shifted only marginally.
FEMS Microbiology Ecology, 1994
The diversity of bacterial communities in deep marine sediments, up to 503 metres below the sea floor of the Japan Sea, was investigated by sequence analysis of amplified 16S rRNA genes. The use of different sample handling procedures greatly affected the types and diversity of sequences obtained. DNA from sediment samples stored aerobically for up to 24 h before freezing was dominated by sequences belonging to the/3-and y-proteobacteria, many of which appeared to originate from aerobic bacteria. Sub-samples equilibrated anaerobically at 16°C, were then injected with a radiotracer and immediately frozen, to simulate the conditions of a typical control sample from a radiotracer based activity assay, contained mostly a-proteobacterial sequences. Pristine sediment samples taken anaerobically and frozen within 2 h contained the widest diversity of sequences from ~-, 3'-, 8-proteobacteria and Gram-positive bacteria, which appeared to have originated from predominantly anaerobic or facultative bacteria. It was clear that both samples that were not frozen immediately (within 2 h) showed signs of enrichment of specific bacterial groups. Our results strongly suggest that immediate freezing should always be employed when sediment samples are to be used to assess bacterial diversity by molecular methods.
Microbial Ecology, 2005
16S rRNA gene-based molecular analyses revealed the presence of several large and so far uncultivated clades within class c-Proteobacteria, designated c-proteobacterial marine sediment (GMS) clades 1 to 4, in marine sediment. The GMS clades appear only indigenous to marine sediment and so far have an unknown functionality. SYBR Green-based real-time PCR analyses using GMS clade-specific primers indicated GMS clades were a significant part of the bacterial community (0.3-8.7% of total 16S rRNA genes) in both polar and temperate marine sediment samples. Univariate statistical analyses indicated that GMS clade communities were indistinguishable in two temperate coastal sediment samples even though these possessed very different mean grain sizes, organic contents, and organic loading rates. GMS clade communities were slightly different (p < 0.05) between polar and temperate sites, suggesting that psychrophilic adaptation among GMS clade taxa corresponds only to subtle phylogenetic differences. Similar levels of difference were also observed through a sediment core reflecting that through the sediment core history, which spanned 3000 years, GMS clonal diversity shifted only marginally.
Systematic and Applied Microbiology, 2009
This study is the first culture-independent report on the regional variability of bacterial diversity in oxic sediments from the unexplored southern Cretan margin (SCM). Three main deep basins (water column depths: 2670-3603 m), located at the mouth of two submarine canyons (Samaria Gorge and Paximades Channel) and an adjacent slope system, as well as two shallow upper-slope stations (water column depths: 215 and 520 m), were sampled. A total of 454 clones were sequenced and the bacterial richness, estimated through five clone libraries using rarefaction analysis, ranged from 71 to 296 unique phylotypes. The average sequence identity of the retrieved Cretan margin sequences compared to the 41,000,000 known rRNA sequences was only 93.5%. A diverse range of prokaryotes was found in the sediments, which were represented by 15 different taxonomic groups at the phylum level. The phylogenetic analysis revealed that these new sequences grouped with the phyla Acidobacteria, Planctomycetes, Actinobacteria, Gamma-, Alpha-and Delta-proteobacteria. Only a few bacterial clones were affiliated with Chloroflexi, Bacteroidetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Nitrospirae, Beta-proteobacteria, Lentisphaerae and Dictyoglomi. A large fraction of the retrieved sequences (12%) did not fall into any taxonomic division previously characterized by molecular criteria, whereas four novel division-level lineages, termed candidate division SCMs, were identified. Bacterial community composition demonstrated significant differences in comparison to previous phylogenetic studies. This divergence was mainly triggered by the dominance of Acidobacteria and Actinobacteria and reflected a bacterial community different from that currently known for oxic and pristine marine sediments.
Hydrobiologia, 2007
The influence of the topographical structure of natural coastal marine environments on the composition of culturable microbial communities in marine sediments was analyzed by comparing the composition of the culturable fraction of sedimental bacterial communities from five topographically disparate marine ecosystems. The sampling areas included open, enclosed and semi-closed coastal seas near Nagasaki, Japan. Bacterial identification and phylogenetic analyses based on 16S rDNA gene sequencing showed that 84.0% of the isolated strains belonged to known species. The marine indigenous c-Proteobacteria were significantly higher (P < 0.05) in abundance among the strains isolated from the open coastal seas, but were less abundant in the enclosed and the semi-closed coastal seas. Conversely, the abundance of the low G + C gram-positive bacteria, mainly soil-derived Bacillus species, was significantly higher (P < 0.001) in the enclosed sea than in the open coastal seas. It was found that the composition of the culturable fraction of coastal sediment bacterial communities might be influenced by topographic factors and could be utilized as a microbiological tool for the assessment of the deterioration of environmental conditions in enclosed coastal seas.
Natural Bacterial Assemblages in Deep-Sea Sediments: Towards A Global View
2000
Deep-sea sediments represent a significant sink term in the global carbon budget. Environmental controls on the resident bacterial assemblages. which determine in large part the magnitude of that term, are only poorly understood. In search of the primary constraining factors, we examined existing data on bacterial biomass in sediments across the entire depth range of the oceans, along with a
1999
16S rDNA clone libraries were analysed to investigate the microbial diversity in marine sediments from Sagami Bay (stations SA, water depth of 1159 m, and SB, 1516 m) and Tokyo Bay (station TK, 43 m). A total of 197 clones was examined by amplified rDNA restriction analysis (ARDRA) using three fourbase-specific restriction enzymes (HhaI, RsaI and HaeIII). In SA, 57 RFLP types were detected from 77 clones. In SB, 17 RFLP types were detected from 62 clones. In TK, 21 RFLP types were detected from 58 clones. The genotypic diversity among the three sampling sites was 0958, 0636 and 0821, respectively, indicating that the microbial diversity of SA was higher than at the other two stations. At SA, the most abundant RFLP type constituted 10 % of all clones. The samples from SB and TK had dominant RFLP types which constituted 60 % and 38 % of the total clone libraries, respectively. The community structure of SA included many single-type clones, which were found only once in the clone libraries. This structure contrasted with that of the other two stations. Thirty-seven clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the microbial diversity in the clone libraries. No clones were identical to any of the known 16S rRNA sequences or to each other. All sequences had S848 % similarity to rDNA sequences retrieved from the DNA databases. Sequenced clones fell into five major lineages of the domain Bacteria : the gamma, delta and epsilon Proteobacteria, Gram-positive bacteria and the division Verrucomicrobia. At SA, the Verrucomicrobia and the three subclasses of the Proteobacteria were found. Most clone sequences belonged to the gamma Proteobacteria. The high-GC Gram-positive bacteria and the gamma subclass of the Proteobacteria were common at both SB and TK. Although the depths of SB and TK were very different, the community diversity inferred from ARDRA and the taxonomic position of the dominant clones were similar. All clones belonging to the high-GC Gram-positive bacteria collected from both SB and TK fell into the same cluster and are regarded as members of an unknown actinomycete group. The clone compositions were different at each sampling site, and clones of the gamma Proteobacteria and high-GC Gram-positive bacteria were dominant.