Contrasting community composition of endospores and vegetative Firmicutes in a marine sediment suggests both endogenous and exogenous sources of endospore accumulation

Cupit, Carina; Lomstein, Bente Aagaard; Kjeldsen, Kasper Urup

doi:10.1111/1758-2229.12679

Cited by 22 publications

(14 citation statements)

References 38 publications

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“…In order to determine how the subsurface microbial communities were formed (assembled), we examined datasets collected at high depth‐resolution from shallower sediments. The comparison shows that many of the 'deep' clades are already detected in the uppermost sediment (Cupit et al ., , Fig. A) and can even be detected in RNA extracted from the uppermost 2.5 cm (Klier et al ., ).…”

Section: Microbial Diversitymentioning

confidence: 96%

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Sub‐seafloor biogeochemical processes and microbial life in the Baltic Sea

Jørgensen

Andrén

Marshall

2020

Environmental Microbiology

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The post-glacial Baltic Sea has experienced extreme changes that are archived today in the deep sediments. IODP Expedition 347 retrieved cores down to 100 m depth and studied the climate history and the deep biosphere. We here review the biogeochemical and microbiological highlights and integrate these with other studies from the Baltic seabed. Cell numbers, endospore abundance and organic matter mineralization rates are extremely high. A 100-fold drop in cell numbers with depth results from a small difference between growth and mortality in the ageing sediment. Evidence for growth derives from a D:L amino acid racemization model, while evidence for mortality derives from the abundance and potential activity of lytic viruses. The deep communities assemble at the bottom of the bioturbated zone from the founding surface community by selection of organisms suited for life under deep sediment conditions. The mean catabolic per-cell rate of microorganisms drops steeply with depth to a life in slow-motion, typical for the deep biosphere. The subsurface life under extreme energy limitation is facilitated by exploitation of recalcitrant substrates, by biochemical protection of nucleic acids and proteins and by repair mechanisms for random mismatches in DNA or damaged amino acids in proteins.

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Section: Microbial Diversitymentioning

confidence: 96%

“…Reads were randomly subsampled to equal sequencing depth to make comparable richness values. (Data available under NCBI/EBI BioProject ID PRJNA377833, from Cupit et al, ). [Color figure can be viewed at http://wileyonlinelibrary.com]…”

Section: Microbial Diversitymentioning

confidence: 99%

Sub‐seafloor biogeochemical processes and microbial life in the Baltic Sea

Jørgensen

Andrén

Marshall

2020

Environmental Microbiology

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“…Firmicutes were observed in all sample groups and were the major phyla in ST, including Bacilli , Clostridia, and Erysipelotrichia (Figure S2) (larger than 60%). Storage tank sludge had less nutrition and a bad environment; Firmicutes could produce endospores and survive in extreme conditions [30]. However, Firmicutes became less competitive when the carbon source was sufficient, making Proteobacteria the dominant phylum in VF and WH.…”

Section: Resultsmentioning

confidence: 99%

Changes in the Microbial Community Diversity of Oil Exploitation

Liu

Lin

et al. 2019

Genes

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To systematically evaluate the ecological changes of an active offshore petroleum production system, the variation of microbial communities at several sites (virgin field, wellhead, storage tank) of an oil production facility in east China was investigated by sequencing the V3 to V4 regions of 16S ribosomal ribonucleic acid (rRNA) of microorganisms. In general, a decrease of microbial community richness and diversity in petroleum mining was observed, as measured by operational taxonomic unit (OTU) numbers, α (Chao1 and Shannon indices), and β (principal coordinate analysis) diversity. Microbial community structure was strongly affected by environmental factors at the phylum and genus levels. At the phylum level, virgin field and wellhead were dominated by Proteobacteria, while the storage tank had higher presence of Firmicutes (29.3–66.9%). Specifically, the wellhead displayed a lower presentence of Proteobacteria (48.6–53.4.0%) and a higher presence of Firmicutes (24.4–29.6%) than the virgin field. At the genus level, the predominant genera were Ochrobactrum and Acinetobacter in the virgin field, Lactococcus and Pseudomonas in the wellhead, and Prauseria and Bacillus in the storage tank. Our study revealed that the microbial community structure was strongly affected by the surrounding environmental factors, such as temperature, oxygen content, salinity, and pH, which could be altered because of the oil production. It was observed that the various microbiomes produced surfactants, transforming the biohazard and degrading hydro-carbon. Altering the microbiome growth condition by appropriate human intervention and taking advantage of natural microbial resources can further enhance oil recovery technology.

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“…Strikingly, while the sediment community shifted during storage and preincubation to a majority of Clostridiales ( Firmicutes ), the OM amendment resulted in activity of the main original groups present in the deeper sediment layers ( Figure 2 ). Members of the Firmicutes form the known endospore communities in Baltic Sea sediments ( Cupit et al, 2019 ). While it is not likely that we have retrieved difficult-to-extract endospore DNA, it is possible that their presence in high relative abundance indicates a life strategy adjusted to survival in conditions not favorable to other organisms.…”

Section: Discussionmentioning

confidence: 99%

Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments

et al. 2021

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Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of 13C and/or 15N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.

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Contrasting community composition of endospores and vegetative Firmicutes in a marine sediment suggests both endogenous and exogenous sources of endospore accumulation

Cited by 22 publications

References 38 publications

Sub‐seafloor biogeochemical processes and microbial life in the Baltic Sea

Sub‐seafloor biogeochemical processes and microbial life in the Baltic Sea

Changes in the Microbial Community Diversity of Oil Exploitation

Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments

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