IMG: the integrated microbial genomes database and comparative analysis system

Markowitz, Victor; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia; Kyrpides, Nikos C.

doi:10.1093/nar/gkr1044

Cited by 1,161 publications

(1,092 citation statements)

References 36 publications

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“…The gyrB database is composed of 30,525 sequences retrieved from 30,175 genomic sequences available in the IMG database v4 (Markowitz et al 2012). According to the gANI cliques defined previously by Varghese and collaborators (Varghese et al 2015), the gyrB marker has the best precision (0.964) and sensitivity (0.955) at a genetic distance of 0.02 (Barret et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Assembly of seed-associated microbial communities within and across successive plant generations

et al. 2017

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Background and aims Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.Methods Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model. Results Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota. Conclusions These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.

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Section: Discussionmentioning

confidence: 99%

Assembly of seed-associated microbial communities within and across successive plant generations

et al. 2017

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“…We searched the Integrated Microbial Genomes (IMG) database (40) for HopAF1 homologs and found them in 148 sequenced bacterial genomes: 106 Pseudomonas, 36 Xanthomonas, four Ralstonia, and two Acidovorax genomes. They are found in two copies in 11 Xanthomonas and 21 Pseudomonas genomes.…”

Section: Evidence For Three Gene-duplication Events In Hopaf1 Evolutimentioning

confidence: 99%

Pseudomonas syringae type III effector HopAF1 suppresses plant immunity by targeting methionine recycling to block ethylene induction

Washington

Mukhtar

Finkel

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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HopAF1 is a type III effector protein of unknown function encoded in the genomes of several strains of Pseudomonas syringae and other plant pathogens. Structural modeling predicted that HopAF1 is closely related to deamidase proteins. Deamidation is the irreversible substitution of an amide group with a carboxylate group. Several bacterial virulence factors are deamidases that manipulate the activity of specific host protein substrates. We identified Arabidopsis methylthioadenosine nucleosidase proteins MTN1 and MTN2 as putative targets of HopAF1 deamidation. MTNs are enzymes in the Yang cycle, which is essential for the high levels of ethylene biosynthesis in Arabidopsis. We hypothesized that HopAF1 inhibits the host defense response by manipulating MTN activity and consequently ethylene levels. We determined that bacterially delivered HopAF1 inhibits ethylene biosynthesis induced by pathogenassociated molecular patterns and that Arabidopsis mtn1 mtn2 mutant plants phenocopy the effect of HopAF1. Furthermore, we identified two conserved asparagines in MTN1 and MTN2 from Arabidopsis that confer loss of function phenotypes when deamidated via site-specific mutation. These residues are potential targets of HopAF1 deamidation. HopAF1-mediated manipulation of Yang cycle MTN proteins is likely an evolutionarily conserved mechanism whereby HopAF1 orthologs from multiple plant pathogens contribute to disease in a large variety of plant hosts.

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“…Community composition profiles were generated with CommunityM by mapping reads onto a database of bacterial, archaeal and eukaryotic 16S and 18S rRNA genes (that is, the SILVA 39 and GreenGenes 40 databases clustered at 97% similarity). To infer the phylogeny of WPS-2 and AD3, a genome tree was generated using 38 universal conserved marker genes 41 from 4,624 bacterial and archaeal genomes retrieved from the Integrated Microbial Genomes database (IMG) 42 together with the recovered population genomes. A concatenated alignment of the marker genes was used to generate the genome tree with FastTree 43 and the tree was visualized in iTOL 44 .…”

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confidence: 99%

Atmospheric trace gases support primary production in Antarctic desert surface soil

Greening

Vanwonterghem

et al. 2017

Nature

302

306

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Cultivation-independent surveys have shown that the desert soils of Antarctica harbour surprisingly rich microbial communities 1-3 . Given that phototroph abundance varies across these Antarctic soils 2,4 , an enduring question is what supports life in those communities with low photosynthetic capacity 3,5 . Here we provide evidence that atmospheric trace gases are the primary energy sources of two Antarctic surface soil communities. We reconstructed 23 draft genomes from metagenomic reads, including genomes from the candidate bacterial phyla WPS-2 and AD3. The dominant community members encoded and expressed high-affinity hydrogenases, carbon monoxide dehydrogenases, and a RuBisCO lineage known to support chemosynthetic carbon fixation 6,7 . Soil microcosms aerobically scavenged atmospheric H 2 and CO at rates sufficient to sustain their theoretical maintenance energy and mediated substantial levels of chemosynthetic but not photosynthetic CO 2 fixation. We propose that atmospheric H 2 , CO 2 and CO provide dependable sources of energy and carbon to support these communities, which suggests that atmospheric energy sources can provide an alternative basis for ecosystem function to solar or geological energy sources 8,9 . Although more extensive sampling is required to verify whether this process is widespread in terrestrial Antarctica and other oligotrophic habitats, our results provide new understanding of the minimal nutritional requirements for life and open the possibility that atmospheric gases support life on other planets.Terrestrial Antarctica is among the most extreme environments on Earth. Its inhabitants experience the cumulative stresses of freezing temperatures, limited carbon, nitrogen and water availability, strong UV radiation, and frequent freeze-thaw cycles 2,10,11 . Although it was once believed that these conditions restrict life, we now know that the continent hosts a surprising diversity of macrofauna and microbiota 1,2,12 . Surveys indicate that the phylum-level composition of microbial communities in Antarctic soils is similar to those of temperate soils 3 , but Antarctic communities are highly specialized at the species level and strongly structured by physicochemical factors 1,3,10 . In many Antarctic soils, microorganisms are thought to live in dormant states 2 , with metabolic energy directed towards cell maintenance rather than growth 13 . However, it is unclear how these communities obtain the energy and carbon needed for maintenance, given that these soils are often low in organic carbon and contain few classical primary producers 2,5 .

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IMG: the integrated microbial genomes database and comparative analysis system

Cited by 1,161 publications

References 36 publications

Assembly of seed-associated microbial communities within and across successive plant generations

Assembly of seed-associated microbial communities within and across successive plant generations

Pseudomonas syringae type III effector HopAF1 suppresses plant immunity by targeting methionine recycling to block ethylene induction

Atmospheric trace gases support primary production in Antarctic desert surface soil

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