Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

Hettich, Robert L.; Sharma, Ritin; Chourey, Karuna; Giannone, Richard J.

doi:10.1016/j.mib.2012.04.008

Cited by 82 publications

(59 citation statements)

References 66 publications

(54 reference statements)

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“…Metaproteomics also have great potential for studies of marine extracellular enzymes, vesicles, and cell surface proteinaceous determinants of surface-associated microbiota. In addition to the identification of surface-induced gene expression and functional adaptivity, metatranscriptomic and metaproteomic approaches show the potential to identify finescale spatiotemporal dynamics and interspecies interactions (such as cooperation and competition) in complex microbial communities (870,871), suitable for process and functional analyses of surface-associated microbiota.…”

Section: Future Perspectives On Studies Of Marine Surface-associated mentioning

confidence: 99%

Microbial Surface Colonization and Biofilm Development in Marine Environments

Dang

Lovell

2016

Microbiol Mol Biol Rev

837

636

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SUMMARYBiotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

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Section: Future Perspectives On Studies Of Marine Surface-associated mentioning

confidence: 99%

Microbial Surface Colonization and Biofilm Development in Marine Environments

Dang

Lovell

2016

Microbiol Mol Biol Rev

837

636

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“…Experimentally, divergent structural proteins from cultivated viral isolates have been annotated using mass spectrometry (MS)-based proteomics (13,(18)(19)(20). Metaproteomics has now emerged as a powerful tool to investigate microbial communities (21,22), and here we apply this approach to marine viral communities to identify virionassociated proteins and facilitate annotation of the structural components of viral dark matter, generating new insights regarding the structural proteins in natural viral communities.…”

Section: Significancementioning

confidence: 99%

Illuminating structural proteins in viral “dark matter” with metaproteomics

Brum

Ignacio‐Espinoza

Kim

et al. 2016

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

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Viruses are ecologically important, yet environmental virology is limited by dominance of unannotated genomic sequences representing taxonomic and functional "viral dark matter." Although recent analytical advances are rapidly improving taxonomic annotations, identifying functional dark matter remains problematic. Here, we apply paired metaproteomics and dsDNA-targeted metagenomics to identify 1,875 virion-associated proteins from the ocean. Over onehalf of these proteins were newly functionally annotated and represent abundant and widespread viral metagenome-derived protein clusters (PCs). One primarily unannotated PC dominated the dataset, but structural modeling and genomic context identified this PC as a previously unidentified capsid protein from multiple uncultivated tailed virus families. Furthermore, four of the five most abundant PCs in the metaproteome represent capsid proteins containing the HK97-like protein fold previously found in many viruses that infect all three domains of life. The dominance of these proteins within our dataset, as well as their global distribution throughout the world's oceans and seas, supports prior hypotheses that this HK97-like protein fold is the most abundant biological structure on Earth. Together, these culture-independent analyses improve virion-associated protein annotations, facilitate the investigation of proteins within natural viral communities, and offer a high-throughput means of illuminating functional viral dark matter.viruses | marine | proteins

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“…1). As with metagenomics and metatranscriptomics, there has been a steady evolution of the methodology for the extraction and analysis of proteins from soils (Bastida et al, 2009;Hettich et al, 2012;Siggins et al, 2012). Nonetheless, the extraction of proteins lags behind that of nucleic acids, in part because of the strong interactions between proteins and other organic molecules and inorganic minerals in soils (Adamczyk et al, 2008; Kleber et al, 2007).…”

Section: Metaproteomicsmentioning

confidence: 99%

The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes

Myrold

Zeglin

Jansson

2013

Soil Sci. Soc. Am. j.

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Technological advances in sequencing technologies and bioinformatics analysis tools now enable the generation of a metagenome from soil, although the ultimate goal of obtaining the entire complement of all genes of all organisms in a given sample of soil still lies in the future. The rich information obtained from a soil metagenome will undoubtedly provide new insights into the taxonomic and functional diversity of soil microorganisms; the question is whether it will also yield greater understanding of how c, n, and other nutrients cycle in soil. The purpose of this review is to describe the steps involved in producing a soil metagenome, including some of the potential pitfalls associated with its production and annotation. Possible solutions to some of these challenges are presented. Selected examples from published soil metagenomic studies are discussed, with an emphasis on clues that they have provided about biogeochemical cycling.Abbreviations: bp, base pairs; DNA, deoxyribonucleic acid; mRNA, messenger ribonucleic acid; RNA, ribonucleic acid; rRNA, ribosomal ribonucleic acid.

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Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

Cited by 82 publications

References 66 publications

Microbial Surface Colonization and Biofilm Development in Marine Environments

Microbial Surface Colonization and Biofilm Development in Marine Environments

Illuminating structural proteins in viral “dark matter” with metaproteomics

The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes

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