Filamentous anoxygenic phototrophic bacteria from cyanobacterial mats of Alla hot springs (Barguzin Valley, Russia)

Gaisin, Vasil A.; Kalashnikov, A. M.; Сухачева, М. В.; Намсараев, З. Б.; Barhutova, Darima D.; Горленко, В. М.; Кузнецов, Б. Б.

doi:10.1007/s00792-015-0777-7

Cited by 23 publications

(18 citation statements)

References 32 publications

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“…Currently, there are many primer systems used to study bacteria that share some functional trait (42–46). For instance, genes encoding two reaction center proteins, PufLM (47, 48) and the Fenna-Matthews-Olson-protein (FmoA) (49) are used to study bacterial photosynthesis, whereas ammonia monooxygenase ( amoCAB ) genes (50) are mostly applied to investigate ammonia-oxidizing archaea. However, there is no universal primer system for all MTB, even though these bacteria have magnetosome mineralization genes that could serve as primer targets.…”

Section: Discussionmentioning

confidence: 99%

Biodiversity of Magnetotactic Bacteria in the Freshwater Lake Beloe Bordukovskoe, Russia

Koziaeva

Alekseeva

Uzun

et al. 2019

Preprint

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20Magnetotactic bacteria (MTB) belong to different taxonomic groups according to 16S 21 rRNA or whole-genome phylogeny. Magnetotactic representatives of the class 22 Alphaproteobacteria and the order Magnetococcales are the most frequently isolated 23 MTB in environmental samples. This bias is due in part to limitations of currently 24 2 available methods to isolate MTB. Here we describe a new approach for isolation of 25 MTB cells that does not depend on cell motility and will allow collecting bacteria 26 both south-and north-seeking movement. We also designed a specific primer system 27 for the gene encoding the MamK protein that effectively detects diverse MTB 28 phylogenetic groups in any sample type. The combination of these two approaches 29 allowed the identification of a novel MTB belonging to the family Syntrophaceae of 30 the class Deltaproteobacteria. Moreover, we found that Nitrospirae bacteria 31 predominated in the MTB fraction of a sample taken from Lake Beloe Bordukovskoe 32 near Moscow, Russia. We describe the novel dominant Nitrospirae bacterium 33 'Candidatus Magnetomonas plexicatena' and propose its taxonomic name. 34 IMPORTANCE 35Among magnetotactic bacteria (MTB), the members of phyla Proteobacteria, 36 Nitrospirae and 'Ca. Omnitrophica' have been studied extensively using the existing 37 approaches. However, in recent years, analyses of the metagenomic databases have 38 revealed the presence of MTB in phylogenetic groups, which had not been previously 39 detected using standard approaches. This finding indicates that the biodiversity of 40 MTB is much broader than is currently known. The difficulty of identifying MTB 41 based on comparative analysis of 16S rRNA genes lies in the existence of closely 42 related species of non-magnetotactic bacteria. Moreover, there is an absence of 16S 43 rRNA MTB sequences from such taxonomic groups as 'Latescibacteria' and 44 Planctomycetes. In addition, the standard methods of separating MTB can benefit 45 bacteria with high motility. Developing novel strategies for investigation offers great 46 3 promise towards identifying MTB groups. We have proposed new approach to 47 separate MTB cells from environmental samples and have also proposed a specific 48 primer system for the MTB identification. 49 INTRODUCTION 50 Prokaryotes having directed active movement that is guided by geomagnetism are 51 collectively called magnetotactic bacteria (MTB) (1). The term MTB has no 52 taxonomic meaning such that it representatives are physiologically, morphologically 53 and phylogenetically different and share only the ability to synthesize special 54 organelles called magnetosomes. Magnetosomes consist of nanosized magnetite 55 (Fe 3 O 4 ) (2) or greigite (Fe 3 S 4 ) (3-5) crystals surrounded by a lipid bilayer membrane 56having proteins specific to the organelle (6, 7). Magnetosomes frequently assemble 57 into chains inside the cell (8). MTB evolved the ability to conduct a special type of 58 movement called magnetotaxis, which is based on orientation relative...

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Section: Discussionmentioning

confidence: 99%

Biodiversity of Magnetotactic Bacteria in the Freshwater Lake Beloe Bordukovskoe, Russia

Koziaeva

Alekseeva

Uzun

et al. 2019

Preprint

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“…In most cases, methods of microbiology were used to describe them. Only the communities of microbial mats of the Alla hot springs were described using molecular biology methods [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Biodiversity of the microbial mat of the Garga hot spring

et al. 2017

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BackgroundMicrobial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0–9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area.ResultsIn this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA.ConclusionsHigh abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that the three studied points sampled at 70 °C, 55 °C, and 45 °C had similar species composition. Cyanobacteria of the genus Leptolyngbya dominated in the upper layer of the microbial mat. Chloroflexi and Chlorobi were less abundant and were mostly observed in the middle part of the microbial mat. We detected domains of heterotrophic organisms in high abundance (Proteobacteria, Firmicutes, Verrucomicrobia, Planctomicetes, Bacteroidetes, Actinobacteria, Thermi), according to metabolic properties of known relatives, which can form complete cycles of carbon, sulphur, and nitrogen in the microbial mat. The studied microbial mats evolved in early stages of biosphere formation. They can live autonomously, providing full cycles of substances and preventing live activity products poisoning.

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“…; Gaisin et al . ). Catechol 2,3 dioxygenases have been related with the degradation of aromatic compounds at high concentration (Hupert‐kocurek and Guzik ); nevertheless, apparently the factors that drive the use of meta or ortho pathways are still unknown because evidences also suggest the participation of catechol 1,2 dioxygenases in communities degrading high concentrations of phenol (Lim et al .…”

Section: Discussionmentioning

confidence: 97%

“…Sequences of the catechol 2,3-dioxygenase were ascribed to the phototrophic Roseiflexus genus. Species of this genus are thermophilic and only putative sequences of catechol 2,3-dioxygenases have been reported (Hanada et al 2002;Suenaga et al 2009;van Der Meer et al 2010;Gaisin et al 2015). Catechol 2,3 dioxygenases have been related with the degradation of aromatic compounds at high concentration (Hupertkocurek and Guzik 2012); nevertheless, apparently the factors that drive the use of meta or ortho pathways are still unknown because evidences also suggest the participation of catechol 1,2 dioxygenases in communities degrading high concentrations of phenol (Lim et al 2013;Bera et al 2017).…”

Section: Discussionmentioning

confidence: 99%

Analysis of a phenol-adapted microbial community: degradation capacity, taxonomy and metabolic description

et al. 2019

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Aims In this study, the ability of the consortium MR‐01 to degrade phenol was determined. The effects of this chemical on the taxonomy and the metabolic behaviour were analysed through metagenomics. Methods and Results Consortium MR‐01 was acclimated in a sublethal concentration of phenol. After this process, the capacity to degrade this molecule was analysed. Results showed that degradation increased with the increment of the initial phenol concentration. Metagenomic analysis indicates that the consortium metabolized phenol under aerobic conditions using phenol 2‐monooxygenase and the meta‐cleavage pathway. Sequence of the enzymes involved in the phenol degradation was ascribed to the Actinomycetales and Chloroflexales orders, with relative abundances <1%. The most abundant genera were part of the Sphingomonadales order; however, the role of these species in the consortium is not clear. Conclusions Consortium MR‐01 degrades efficiently high concentrations of phenol. The participation of extremophiles in the degradation process and the emergence of beneficial metabolic dependencies between the community members are some of the strategies used by the consortium to survive and develop under harsh environmental conditions. Significance and Impact of the Study This is one of the few studies describing the taxonomy and metabolic profile of a phenol degrading consortium.

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Filamentous anoxygenic phototrophic bacteria from cyanobacterial mats of Alla hot springs (Barguzin Valley, Russia)

Cited by 23 publications

References 32 publications

Biodiversity of Magnetotactic Bacteria in the Freshwater Lake Beloe Bordukovskoe, Russia

Biodiversity of Magnetotactic Bacteria in the Freshwater Lake Beloe Bordukovskoe, Russia

Biodiversity of the microbial mat of the Garga hot spring

Analysis of a phenol-adapted microbial community: degradation capacity, taxonomy and metabolic description

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