Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi
Abstract Background Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are fe...
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| Format: | Article |
| Language: | English |
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BMC
2018-10-01
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| Series: | Microbiome |
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| Online Access: | http://link.springer.com/article/10.1186/s40168-018-0563-8 |
| _version_ | 1818325534845698048 |
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| author | Maliheh Mehrshad Michaela M Salcher Yusuke Okazaki Shin-ichi Nakano Karel Šimek Adrian-Stefan Andrei Rohit Ghai |
| author_facet | Maliheh Mehrshad Michaela M Salcher Yusuke Okazaki Shin-ichi Nakano Karel Šimek Adrian-Stefan Andrei Rohit Ghai |
| author_sort | Maliheh Mehrshad |
| collection | DOAJ |
| description | Abstract Background Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11. Results Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway. Conclusions Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion. |
| first_indexed | 2024-12-13T11:46:01Z |
| format | Article |
| id | doaj.art-f77745a100c64040bc715f148cc9b9e8 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-13T11:46:01Z |
| publishDate | 2018-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-f77745a100c64040bc715f148cc9b9e82022-12-21T23:47:30ZengBMCMicrobiome2049-26182018-10-016111310.1186/s40168-018-0563-8Hidden in plain sight—highly abundant and diverse planktonic freshwater ChloroflexiMaliheh Mehrshad0Michaela M Salcher1Yusuke Okazaki2Shin-ichi Nakano3Karel Šimek4Adrian-Stefan Andrei5Rohit Ghai6Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of SciencesLimnological Station, Institute of Plant and Microbial Biology, University of ZurichCenter for Ecological Research, Kyoto UniversityCenter for Ecological Research, Kyoto UniversityInstitute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of SciencesInstitute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of SciencesInstitute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of SciencesAbstract Background Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11. Results Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway. Conclusions Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.http://link.springer.com/article/10.1186/s40168-018-0563-8ChloroflexiFreshwater ecologyMetagenomicsCARD-FISH |
| spellingShingle | Maliheh Mehrshad Michaela M Salcher Yusuke Okazaki Shin-ichi Nakano Karel Šimek Adrian-Stefan Andrei Rohit Ghai Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi Microbiome Chloroflexi Freshwater ecology Metagenomics CARD-FISH |
| title | Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi |
| title_full | Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi |
| title_fullStr | Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi |
| title_full_unstemmed | Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi |
| title_short | Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi |
| title_sort | hidden in plain sight highly abundant and diverse planktonic freshwater chloroflexi |
| topic | Chloroflexi Freshwater ecology Metagenomics CARD-FISH |
| url | http://link.springer.com/article/10.1186/s40168-018-0563-8 |
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