Genome Sequence of
            <i>Halomonas</i>
            sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm

O’Dell, Kaela B.; Woo, Hyun-Joo; Utturkar, Sagar M.; Klingeman, Dawn M.; Brown, Steven D.; Hazen, Terry C.

doi:10.1128/genomea.00402-15

Cited by 8 publications

(7 citation statements)

References 10 publications

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“…Halomonas spp. (Halomonadaceae) are also of interest, since they represent one of the most abundant bacterial genera within the A. vulgare microbiome [ 42 , 51 , 52 ].Their genomes possess several genes encoding LMEs, and they are known to contribute to lignin degradation [ 104 ]. Accordingly, they were identified as major contributors of LMEs in isopods from laboratory lineages.…”

Section: Discussionmentioning

confidence: 99%

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

et al. 2018

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BackgroundWoodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the environment together with other macroarthropods. Lignocellulose is the main component of plants and is composed of cellulose, lignin and hemicellulose. Its digestion requires the action of multiple Carbohydrate-Active enZymes (called CAZymes), typically acting together as a cocktail with complementary, synergistic activities and modes of action. Some invertebrates express a few endogenous lignocellulose-degrading enzymes but in most species, an efficient degradation and digestion of lignocellulose can only be achieved through mutualistic associations with endosymbionts. Similar to termites, it has been suspected that several bacterial symbionts may be involved in lignocellulose degradation in terrestrial isopods, by completing the CAZyme repertoire of their hosts.ResultsTo test this hypothesis, host transcriptomic and microbiome shotgun metagenomic datasets were obtained and investigated from the pill bug Armadillidium vulgare. Many genes of bacterial and archaeal origin coding for CAZymes were identified in the metagenomes of several host tissues and the gut content of specimens from both laboratory lineages and a natural population of A. vulgare. Some of them may be involved in the degradation of cellulose, hemicellulose, and lignin. Reconstructing a lignocellulose-degrading microbial community based on the prokaryotic taxa contributing relevant CAZymes revealed two taxonomically distinct but functionally redundant microbial communities depending on host origin. In parallel, endogenous CAZymes were identified from the transcriptome of the host and their expression in digestive tissues was demonstrated by RT-qPCR, demonstrating a complementary enzyme repertoire for lignocellulose degradation from both the host and the microbiome in A. vulgare.ConclusionsOur results provide new insights into the role of the microbiome in the evolution of terrestrial isopods and their adaptive radiation in terrestrial habitats.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0536-y) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

et al. 2018

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“…ILs, however, can be extremely toxic to microbes and enzymes, and IL removal comes at a great expense. Halotolerant microbes or their enzymes have shown great potential to withstand IL concentrations far greater than typical lab strains, and are a potential resource for engineering IL-tolerance in biofuel-producing lab strains (Pottkämper et al, 2009 ; Gunny et al, 2014 ; Portillo and Saadeddin, 2014 ; O'Dell et al, 2015 ). Here we found that Pond A23 had a ten-fold increase in dissolved organic material over that found in Pond 2C (Table 1 ), with a corresponding abundance of CAZy AA genes primarily in the Proteobacteria and Bacteroidetes, as well as genes for low-pI AA proteins in the Euryarchaeota.…”

Section: Discussionmentioning

confidence: 99%

Microbial Community Structure and Functional Potential Along a Hypersaline Gradient

Kimbrel

Ballor

et al. 2018

Front. Microbiol.

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Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants.

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“…Thus the genome analysis explains the ability of KO116 to inhabit insoluble organosolvent lignin and also its tolerance towards ionic solvents. 46 .…”

Section: Whole Genome Sequence Studies Of Lignocellulose Degrading Bamentioning

confidence: 99%

Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms

Kameshwar

Qin

2016

Int. J. Biol. Sci.

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Lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. Lignocellulose is an abundant renewable biomaterial present on the earth. It has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. Microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. Based on the plant materials they degrade these fungi were classified as white rot, brown rot and soft rot. However, some groups of bacteria belonging to the actinomycetes, α-proteobacteria and β-proteobacteria were also found to be efficient in degrading lignocellulosic biomass but not well understood unlike the fungi. In this review we focus on recent advancements deployed for finding and understanding the lignocellulose degradation by microorganisms. Conventional molecular methods like sequencing 16s rRNA and Inter Transcribed Spacer (ITS) regions were used for identification and classification of microbes. Recent progression in genomics mainly next generation sequencing technologies made the whole genome sequencing of microbes possible in a great ease. The whole genome sequence studies reveals high quality information about genes and canonical pathways involved in the lignin and other cell wall components degradation.

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Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm

Cited by 8 publications

References 10 publications

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

Microbial Community Structure and Functional Potential Along a Hypersaline Gradient

Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms

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