Comparative genomics analyses indicate differential methylated amine utilization trait within members of the genus <i>Gemmobacter</i>

Kröber, Eileen; Cunningham, Mark R.; Peixoto, Julianna; Spurgin, Lewis G.; Wischer, Daniela; Krüger, Ricardo Henrique; Kumaresan, Deepak

doi:10.1111/1758-2229.12927

Cited by 9 publications

(8 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This result may indicate that the NMG pathway is more abundant than the MaDH pathway in PPFMs. Previous studies have pointed out that the NMG pathway is highly abundant not only in methylotrophic bacteria ( Kröber et al, 2021a ) but can also be found in non-methylotrophic bacteria, which rely on it as a nitrogen source ( Chen et al, 2010 ). In a metagenomic study on soybean and rice symbionts, the NMG pathway was more abundantly detected than the mau cluster in Methylobacterium ( Minami et al, 2016 ).…”

Section: Resultsmentioning

confidence: 99%

“…Since glyoxylate, which is necessary for the serine cycle, is supplied by the EMC pathway ( Schneider et al, 2012 ), the glyoxylate cycle is missing in the PPFM species, but it is present in the other species in the Methylobacteriaceae family. Among the methylamine-utilizing PPFMs, the NMG pathway seems to be preferred; likewise, the NMG pathway is believed to be the major methylamine utilization pathway in soybean-associated Methylobacterium ( Minami et al, 2016 ) and other methylotrophic bacteria or non-methylotrophic bacteria ( Chen et al, 2010 ; Kröber et al, 2021a ).…”

Section: Discussionmentioning

confidence: 99%

“…oryzae and Mb. phyllosphaerae as the same species ( Green and Ardley, 2018 ; Hördt et al, 2020 ; Kröber et al, 2021a ). Here we also propose reclassifying Mb.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

et al. 2021

View full text Add to dashboard Cite

The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Methylocystis [92] Methylovulum [189] Methylotrophy Gemmobacter [190] OM43 clade [191] Extracellular polymeric substance (EPS) secretion Terrimonas [192] Biosorption of heavy metals Sphaerotilus [193] The majority of the fungi present within the samples collected from TD1 were fungi that function in decomposition, e.g., Avachytrium, Entophlyctis, Glutinoglossum. Other fungi were those known to be involved in (1) parasitism in algae, amoebae, and other fungi, (2) plant-fungal interaction, (3) predation, and even (4) mutualism as in the lichen-forming fungi (Table 2).…”

Section: Methane Oxidationmentioning

confidence: 99%

Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand

Ruen-Pham

Graham

Satjarak

2021

Plants

View full text Add to dashboard Cite

Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.

show abstract

“…b Genomic distribution of potential biomarker genes involved in metal transformation in methanotrophs. Presence/absence of biomarker genes are mapped to a phylogenomic tree constructed using 74 single-copy marker genes specific to Bacteria via the GtoTree (v1.5.22) pipeline (as described in [ 135 ]). Protein sequences were retrieved using HMMER3 tool and multiple alignments were produced using MUSCLE (v.3.8.31, default settings).…”

Section: Introductionmentioning

confidence: 99%

Metal(loid) speciation and transformation by aerobic methanotrophs

et al. 2021

Self Cite

View full text Add to dashboard Cite

Manufacturing and resource industries are the key drivers for economic growth with a huge environmental cost (e.g. discharge of industrial effluents and post-mining substrates). Pollutants from waste streams, either organic or inorganic (e.g. heavy metals), are prone to interact with their physical environment that not only affects the ecosystem health but also the livelihood of local communities. Unlike organic pollutants, heavy metals or trace metals (e.g. chromium, mercury) are non-biodegradable, bioaccumulate through food-web interactions and are likely to have a long-term impact on ecosystem health. Microorganisms provide varied ecosystem services including climate regulation, purification of groundwater, rehabilitation of contaminated sites by detoxifying pollutants. Recent studies have highlighted the potential of methanotrophs, a group of bacteria that can use methane as a sole carbon and energy source, to transform toxic metal (loids) such as chromium, mercury and selenium. In this review, we synthesise recent advances in the role of essential metals (e.g. copper) for methanotroph activity, uptake mechanisms alongside their potential to transform toxic heavy metal (loids). Case studies are presented on chromium, selenium and mercury pollution from the tanneries, coal burning and artisanal gold mining, respectively, which are particular problems in the developing economy that we propose may be suitable for remediation by methanotrophs.

show abstract

Comparative genomics analyses indicate differential methylated amine utilization trait within members of the genus Gemmobacter

Cited by 9 publications

References 74 publications

Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand

Metal(loid) speciation and transformation by aerobic methanotrophs

Contact Info

Product

Resources

About