Genomics of Aerobic Photoheterotrophs in Wheat Phyllosphere Reveals Divergent Evolutionary Patterns of Photosynthetic Genes in Methylobacterium spp.

Zervas, Athanasios; Zeng, Yonghui; Madsen, Anne Mette; Hansen, Lars

doi:10.1093/gbe/evz204

Cited by 22 publications

(22 citation statements)

References 39 publications

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“…All target colonies were subjected to MALDI-TOF MS fingerprinting analysis using the Microflex LT system (Bruker Daltonics, Bremen, Germany) following the procedure described previously ( Zervas et al, 2019 ). Briefly, a toothpick was used to transfer a small amount of a test colony onto the target plate (MSP 96 polished steel, Bruker), which was evenly spread out and formed a thin layer of biomass on the steel plate.…”

Section: Methodsmentioning

confidence: 99%

Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes

Zeng

Nupur

et al. 2021

Front. Microbiol.

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The bacterial phylum Gemmatimonadetes contains members capable of performing bacteriochlorophyll-based phototrophy (chlorophototrophy). However, only one strain of chlorophototrophic Gemmatimonadetes bacteria (CGB) has been isolated to date, hampering our further understanding of their photoheterotrophic lifestyle and the evolution of phototrophy in CGB. By combining a culturomics strategy with a rapid screening technique for chlorophototrophs, we report the isolation of a new member of CGB, Gemmatimonas (G.) groenlandica sp. nov., from the surface water of a stream in the Zackenberg Valley in High Arctic Greenland. Distinct from the microaerophilic G. phototrophica strain AP64T, G. groenlandica strain TET16T is a strictly aerobic anoxygenic phototroph, lacking many oxygen-independent enzymes while possessing an expanded arsenal for coping with oxidative stresses. Its pigment composition and infra-red absorption properties are also different from G. phototrophica, indicating that it possesses a different photosystem apparatus. The complete genome sequence of G. groenlandica reveals unique and conserved features in the photosynthesis gene clusters of CGB. We further analyzed metagenome-assembled genomes of CGB obtained from soil and glacier metagenomes from Northeast Greenland, revealing a wide distribution pattern of CGB beyond the stream water investigated.

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Section: Methodsmentioning

confidence: 99%

Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes

Zeng

Nupur

et al. 2021

Front. Microbiol.

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“…We included 29 genomes from Methylobacterium type strains recently sequenced (Alessa et al ., 2021; Bijlani et al ., 2021), hence covering most Methylobacterium species described so far. We also included 38 genomes available from two large surveys of the Arabidopsis and wheat phyllospheres (Helfrich et al ., 2018; Zervas et al ., 2019), and sequenced 24 additional genomes of isolates from a large survey of the temperate forest phyllosphere (Leducq et al ., 2022), hence extending our dataset to the leaf-associated Methylobacterium diversity. The 24 newly assembled genomes had 41 to 405 scaffolds (depth: 188-304x) for a total size (5-7Mb) and average GC content (67-70%) in the expected range for Methylobacterium genomes (Dataset S2).…”

Section: Resultsmentioning

confidence: 99%

“…We included 29 genomes from Methylobacterium type strains recently published (Alessa et al, 2021;Bijlani et al, 2021) in order to cover most Methylobacterium species described so far. We also included 38 genomes available from two large surveys of the Arabidopsis and wheat phyllospheres (Helfrich et al, 2018;Zervas et al, 2019) and sequenced 24 additional genomes (see next section) of isolates from a large survey of the temperate forest phyllosphere (Leducq et al, 2022), hence extending our dataset to the leaf-associated Methylobacterium diversity.…”

Section: Methylobacteriaceae Genome Collectionmentioning

confidence: 99%

Comprehensive phylogenomics of Methylobacterium reveals four evolutionary distinct groups and underappreciated phyllosphere diversity

Leducq

Sneddon

Santos

et al. 2022

Preprint

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Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well-studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere, and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfers. We showed that Methylobacterium contains four evolutionary distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition of recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), which early branching in Methylobacterium history was heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandon of Methylorubrum.

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“…It was able to reliably and repeatedly obtain >6.5 Gb of long−read sequencing data with a mean read length of 13 kb and an N50 of 26 kb (Schalamun et al, 2019). Other examples of MinION application in agriculture and forestry include detection of pathogenic fungi (Cui et al, 2019;Hu et al, 2019;Rajarammohan et al, 2019;Srivastava et al, 2019;Purushotham et al, 2020), bacteria (Badial et al, 2018;Krehenwinkel et al, 2019;Zervas et al, 2019;Fujiyoshi et al, 2020), viruses (van der Merwe et al, 2017Filloux et al, 2018;Boykin et al, 2019;Della Bartola et al, 2020), and nematodes (Eccles et al, 2018;Knot et al, 2020).…”

Section: Poc Sequencingmentioning

confidence: 99%

Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry

Baldi

Porta

2020

Front. Plant Sci.

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Early detection of plant diseases is a crucial factor to prevent or limit the spread of a rising infection that could cause significant economic loss. Detection test on plant diseases in the laboratory can be laborious, time consuming, expensive, and normally requires specific technical expertise. Moreover, in the developing countries, it is often difficult to find laboratories equipped for this kind of analysis. Therefore, in the past years, a high effort has been made for the development of fast, specific, sensitive, and cost-effective tests that can be successfully used in plant pathology directly in the field by low-specialized personnel using minimal equipment. Nucleic acid-based methods have proven to be a good choice for the development of detection tools in several fields, such as human/animal health, food safety, and water analysis, and their application in plant pathogen detection is becoming more and more common. In the present review, the more recent nucleic acid-based protocols for point-of-care (POC) plant pathogen detection and identification are described and analyzed. All these methods have a high potential for early detection of destructive diseases in agriculture and forestry, they should help make molecular detection for plant pathogens accessible to anyone, anywhere, and at any time. We do not suggest that on-site methods should replace lab testing completely, which remains crucial for more complex researches, such as identification and classification of new pathogens or the study of plant defense mechanisms. Instead, POC analysis can provide a useful, fast, and efficient preliminary on-site screening that is crucial in the struggle against plant pathogens.

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Genomics of Aerobic Photoheterotrophs in Wheat Phyllosphere Reveals Divergent Evolutionary Patterns of Photosynthetic Genes in Methylobacterium spp.

Cited by 22 publications

References 39 publications

Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes

Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes

Comprehensive phylogenomics of Methylobacterium reveals four evolutionary distinct groups and underappreciated phyllosphere diversity

Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry

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