Taxonomic Diversity of the Microbial Biofilms Collected along the Thermal Streams on Kunashir Island

Malygina, Alexandra; Balkin, Alexander S.; Polyakova, Elena; Stefanov, Sergey; Потехин, А. А.; Gogoleva, Natalia

doi:10.3390/ecologies4010009

Cited by 5 publications

(2 citation statements)

References 79 publications

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“…Occasionally, light grey or whitish fibrous biofilm is also present alongside the brown biofilm, possible linked to four Aquificaceae -like MAGs. This fibrous biofilm resembles the one documented in thermal streams in Russia [ 38 ]. In the constructed MAGs, we identified Type IV twitching motility protein PilT, PilT/PilU family pilus ATPase, pilus assembly protein PilM (closely related to Hydrogenobacter type), pilus assembly protein, and pre-pilin peptidase.…”

Section: Resultssupporting

confidence: 55%

Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation

Liew,

Shahar,

Shamsir

et al. 2024

Environmental Microbiome

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Background Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58–74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism. Results Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures. Conclusions This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.

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Section: Resultssupporting

confidence: 55%

Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation

Liew,

Shahar,

Shamsir

et al. 2024

Environmental Microbiome

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“…Attempts to isolate Aigarchaeota and Candidatus C. subterraneum have thus far been unsuccessful [25,31]. Abundance of sequences related the Candidatus C. subterraneum in sediment samples was similar to mat samples indicating that this archaeon might accumulate and thrive in mat or sediments where they may depend on other microbial communities for growth.…”

Section: Discussionmentioning

confidence: 99%

Field deployable automated nucleic acid extraction system enables rapid on-site measurement of microbial diversity of Yellowstone National Park hot springs

Wood,

Urbaniak,

Parker

et al. 2023

Preprint

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Background: Microbial diversity estimation relies heavily on the extraction of nucleic acids from complex sample matrixes, regardless of the location of the laboratory used to recover the DNA, including those on Earth or in space. Nucleic acid sample preparation steps are labor intensive and require the effective lysis of cells and recovery of pure inhibitor free purification prior to downstream applications. An automated system is desirable for field deployment because easy of use and autonomous rapid results. This extends to use in remote filed locations by NASA for the in situ measurements of life. The goal of this study was to setup a field-deployable lab in a remote setting with limited resources and demonstrate the ability to process and sequence nucleic acid samples on-site. Microbial mat and sediment samples were collected from several hot springs in Yellowstone National Park (YNP), targeting the Five Sister Springs (FSS), spring LNN010, and Octopus Spring (OS). Samples were processed on site and analyzed for microbial diversity using the field-deployable lab instrument. Results: Microbial diversity measured with both the Illumina (short reads) and Oxford Nanopore Technology (ONT; long reads) sequencing systems was highly similar. In general, for both the FSS and OS hot spring sites, bacteria (>90%) dominated over archaea (<10%). Metagenomic results were binned to existing databases such that the taxonomic ID represents the closest known organism with a sequenced genome. With this caveat the presence of, the most common archaeal community member in both the mat and sediment was related to Candidatus Caldiarchaeum subterraneum. Among the bacterial members, Roseiflexus sp. RS-1 was found to be highly abundant in the mat environment, as already reported. Notably, however, organisms related to Bacterium HR17 was abundant several FSS/OS mat samples. The detection of this novel bacterial community member warrants additional research. Conclusion: This is the first study to deploy an automated nucleic acid extraction system in YNP) to rapidly (~8 to 9 hrs) measure the environmental microbiome of hot springs. The demonstration of a field deployable system for nucleic acids extraction from complex materials (mats and sediments) highlights its utility not only in extreme environments on Earth but its potential benefit to NASA and deployment in space, once performance under microgravity is refined. The benefits of this new field-deployable lab include sample processing (extracting nucleic acids), shotgun metagenome library preparation, and sequencing utilizing the space-tested Nanopore sequencing platform.

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New viruses infecting hyperthermophilic bacteriumThermus thermophilus

Kolesnik,

Pavlov,

Demkina

et al. 2024

Preprint

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Highly diverse phages infecting thermophilic bacteria of theThermusgenus have been isolated over the years from hot springs around the world. Many of these phages are unique, rely on highly unusual developmental strategies, and encode novel enzymes. The variety ofThermusphages is clearly undersampled, as evidenced, for example, by a paucity of phage-matching spacers inThermusCRISPR arrays. Using water samples collected from hot springs in the Kunashir Island from the Kuril archipelago and from the Tsaishi and Nokalakevi districts in the Republic of Georgia we isolated several distinct phages infecting laboratory strains ofThermus thermophilus. Genomic sequence analysis of 11 phages revealed both close relatives of previously describedThermusphages isolated from geographically distant sites, as well as phages with very limited similarity to earlier isolates. Comparative analysis allowed us to predict several accessory phage genes whose products may be involved in host defense/interviral warfare, including a putative Type V CRISPR-cassystem.

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Taxonomic Diversity of the Microbial Biofilms Collected along the Thermal Streams on Kunashir Island

Cited by 5 publications

References 79 publications

Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation

Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation

Field deployable automated nucleic acid extraction system enables rapid on-site measurement of microbial diversity of Yellowstone National Park hot springs

New viruses infecting hyperthermophilic bacteriumThermus thermophilus

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