Candidate OP Phyla: Importance, Ecology and Cultivation Prospects

Kumar, Mukul; Saravanan, Venkatakrishnan Sivaraj

doi:10.1007/s12088-011-0144-z

Cited by 8 publications

(4 citation statements)

References 18 publications

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“…This might explain the dominance of Phyllobacterium in ATII-I, due to being a hydrocarbon-rich layer (Burke et al, 1981 ; Faber et al, 1998 ; Schmidt et al, 2003 ). The Kebrit brine-seawater interface layers (KB-U and KB-L) were mainly dominated by the marine Candidatus taxa OP3 and SAR406 (Gordon and Giovannoni, 1996 ; Glockner et al, 2010 ; Kumar and Saravanan, 2010 ). The Candidatus OD1 phylum (dominant in KB-L) is known to occur in marine environments characterized by notable concentrations of sulfur compounds (Harris et al, 2004 ).…”

Section: Discussionmentioning

confidence: 99%

Aerobic methanotrophic communities at the Red Sea brine-seawater interface

et al. 2014

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The central rift of the Red Sea contains 25 brine pools with different physicochemical conditions, dictating the diversity and abundance of the microbial community. Three of these pools, the Atlantis II, Kebrit and Discovery Deeps, are uniquely characterized by a high concentration of hydrocarbons. The brine-seawater interface, described as an anoxic-oxic (brine-seawater) boundary, is characterized by a high methane concentration, thus favoring aerobic methane oxidation. The current study analyzed the aerobic free–living methane-oxidizing bacterial communities that potentially contribute to methane oxidation at the brine-seawater interfaces of the three aforementioned brine pools, using metagenomic pyrosequencing, 16S rRNA pyrotags and pmoA library constructs. The sequencing of 16S rRNA pyrotags revealed that these interfaces are characterized by high microbial community diversity. Signatures of aerobic methane-oxidizing bacteria were detected in the Atlantis II Interface (ATII-I) and the Kebrit Deep Upper (KB-U) and Lower (KB-L) brine-seawater interfaces. Through phylogenetic analysis of pmoA, we further demonstrated that the ATII-I aerobic methanotroph community is highly diverse. We propose four ATII-I pmoA clusters. Most importantly, cluster 2 groups with marine methane seep methanotrophs, and cluster 4 represent a unique lineage of an uncultured bacterium with divergent alkane monooxygenases. Moreover, non-metric multidimensional scaling (NMDS) based on the ordination of putative enzymes involved in methane metabolism showed that the Kebrit interface layers were distinct from the ATII-I and DD-I brine-seawater interfaces.

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Section: Discussionmentioning

confidence: 99%

Aerobic methanotrophic communities at the Red Sea brine-seawater interface

et al. 2014

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“…Members within the Spirochaetes are core to anaerobic digesters [53] and are known to be syntrophic with methanogens and can outcompete other fermenters, such as Clostridium species [54]. The first environmental clone for OP11 was isolated from the Obsidian Pool in Yellow Stone National Park that is an environment rich in metals and sulfur compounds [55]. OP11-related organisms have been identified at other metal bioremediation sites [56].…”

Section: Co-occurrence Of Taxa In the Bcr Biosolidsmentioning

confidence: 99%

Seasonal Microbial Population Shifts in a Bioremediation System Treating Metal and Sulfate-Rich Seepage

Baldwin¹,

Mattes²,

Rezadehbashi³

et al. 2016

Minerals

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Biochemical reactors (BCRs) using complex organics for bioremediation of mine-influenced water must operate successfully year round. In cold climates, where many mines in Canada are located, survival of the important microorganisms through the winter months is a concern. In this work, broad phylogenetic surveys, using metagenomics, of the microbial populations in pulp mill biosolids used to remediate metal leachate containing As, Zn, Cd and sulfate were performed to see if the types of microorganisms present changed over the seasons of one year (August 2008 to July 2009). Despite temperature variations between 0 and 17˝C the overall structure of the microbial population was fairly consistent. A cyclical pattern in relative abundance was detected in certain taxa. These included fermenter-related groups, which were out of phase with other taxa such as Desulfobulbus that represented potential consumers of fermentation byproducts. Sulfate-reducers in the BCR biosolids were closely related to psychrotolerant species. Temperature was not a factor that shaped the microbial population structure within the BCR biosolids. Kinetics of organic matter degradation by these microbes and the rate of supply of organic carbon to sulfate-reducers would likely affect the metal removal rates at different temperatures.

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“…In an analyses performed by Vick et al ( 2010 ) using three Little Hot Creek (LHC) hot springs samples, the Aquificae and Thermodesulfobacteria phyla dominated samples from LHC1 (82.5°C, pH 6.75) and LHC3 (79°C, pH 6.97). In contrast, the LCH4 hot spring (78.7°C, pH 6.85) was dominated by the candidate divisions OP1 and OP9, which were first identified in YNP Obsidian Pool (Rohini Kumar and Saravanan, 2010 ). Water chemistry parameters such as dissolved sulfate, total nitrogen, organic carbon, pyrite, elemental sulfur, and other metal compounds can also influence microbial diversity, as reported by Huang et al ( 2013 ) and Hou et al ( 2013 ).…”

Section: Introductionmentioning

confidence: 99%

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing

Chan

Tay³

et al. 2015

Front. Microbiol.

150

120

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The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0–9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.

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Candidate OP Phyla: Importance, Ecology and Cultivation Prospects

Cited by 8 publications

References 18 publications

Aerobic methanotrophic communities at the Red Sea brine-seawater interface

Aerobic methanotrophic communities at the Red Sea brine-seawater interface

Seasonal Microbial Population Shifts in a Bioremediation System Treating Metal and Sulfate-Rich Seepage

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing

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