Autotrophic Microbe Metagenomes and Metabolic Pathways Differentiate Adjacent Red Sea Brine Pools

Wang, Yong; Cao, Huiluo; Zhang, Guishan; Bougouffa, Salim; Lee, On On; Al-Suwailem, Abdulaziz M.; Qian, Pei‐Yuan

doi:10.1038/srep01748

Cited by 27 publications

(34 citation statements)

References 51 publications

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“…Comparisons between 2 samples were conducted using the Mann-Whitney U test (44). Raw counts of COG and KEGG functional annotations for the 4 metagenomes were normalized as previously described (43). To generate heat maps of COG and KEGG genes, the normalized numbers were standardized to Z scores and then analyzed using Cluster 3 () (45).…”

Section: Methodsmentioning

confidence: 99%

Microbial Sulfur Cycle in Two Hydrothermal Chimneys on the Southwest Indian Ridge

Cao

Wang

Lee

et al. 2014

mBio

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Sulfur is an important element in sustaining microbial communities present in hydrothermal vents. Sulfur oxidation has been extensively studied due to its importance in chemosynthetic pathways in hydrothermal fields; however, less is known about sulfate reduction. Here, the metagenomes of hydrothermal chimneys located on the ultraslow-spreading Southwest Indian Ridge (SWIR) were pyrosequenced to elucidate the associated microbial sulfur cycle. A taxonomic summary of known genes revealed a few dominant bacteria that participated in the microbial sulfur cycle, particularly sulfate-reducing Deltaproteobacteria. The metagenomes studied contained highly abundant genes related to sulfur oxidation and reduction. Several carbon metabolic pathways, in particular the Calvin-Benson-Bassham pathway and the reductive tricarboxylic acid cycles for CO2 fixation, were identified in sulfur-oxidizing autotrophic bacteria. In contrast, highly abundant genes related to the oxidation of short-chain alkanes were grouped with sulfate-reducing bacteria, suggesting an important role for short-chain alkanes in the sulfur cycle. Furthermore, sulfur-oxidizing bacteria were associated with enrichment for genes involved in the denitrification pathway, while sulfate-reducing bacteria displayed enrichment for genes responsible for hydrogen utilization. In conclusion, this study provides insights regarding major microbial metabolic activities that are driven by the sulfur cycle in low-temperature hydrothermal chimneys present on an ultraslow midocean ridge.

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Section: Methodsmentioning

confidence: 99%

Microbial Sulfur Cycle in Two Hydrothermal Chimneys on the Southwest Indian Ridge

Cao

Wang

Lee

et al. 2014

mBio

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“…Yet, current knowledge of the pelagic microbial community structure of the dark ocean, the largest biome in the biosphere, is based on a pool of samples collected at specific locations (DeLong et al, 2006;Martín-Cuadrado et al, 2007;Brown et al, 2009;Galand et al, 2010;Agogué et al, 2011;Eloe et al, 2011;Quaiser et al, 2011;Smedile et al, 2012;Wang et al, 2013;Wilkins et al, 2013;Ganesh et al, 2014) (Supplementary Figure S1) and thus are dwarf in comparison with the analyses of upper ocean microbial communities, which have indeed been assessed at global scales Yooseph et al, 2007;Zinger et al, 2011;Sunagawa et al, 2015). Whereas the deep ocean is often considered to be a rather uniform environment, the connectivity of pelagic microbial communities may be reduced by the limited mixing between water masses (Agogué et al, 2011;Hamdan et al, 2013) or modulated by advection (Wilkins et al, 2013) imposing limitations on the dispersion of marine microbes in this low-turbulence environment.…”

Section: Introductionmentioning

confidence: 99%

Global diversity and biogeography of deep-sea pelagic prokaryotes

Salazar¹,

et al. 2015

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The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean's microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (~3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered.

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“…Studies of microbial lifestyles in brine pools are less common than those of hydrothermal vents. The brine pools studied so far include the Shaban Deep (Ferrer et al, 2012), Discovery Deep (Wang et al, 2013), Atlantis II Deep (Ngugi et al, 2015), and Kebrit Deep (Guan et al, 2015) of the Red Sea, which contains more than 25 deep hypersaline anoxic pools (Antunes et al, 2011). Previous investigations of other deep-sea brine pools included those in the Mediterranean Sea (van der Wielen et al, 2005) and the Gulf of Mexico (Formolo and Lyons, 2013).…”

Section: Introductionmentioning

confidence: 99%

Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool

et al. 2016

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The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC), and F420H2 dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT). Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs) is a dominant process performed by microorganisms from various phyla within this ecosystem.

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Autotrophic Microbe Metagenomes and Metabolic Pathways Differentiate Adjacent Red Sea Brine Pools

Cited by 27 publications

References 51 publications

Microbial Sulfur Cycle in Two Hydrothermal Chimneys on the Southwest Indian Ridge

Microbial Sulfur Cycle in Two Hydrothermal Chimneys on the Southwest Indian Ridge

Global diversity and biogeography of deep-sea pelagic prokaryotes

Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool

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