Dataset Information

Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil.

ABSTRACT: The addition of glucose to soil has long been used to study the metabolic activity of microbes in soil; however, the response of the microbial ecophysiology remains poorly characterized. To address this, we sequenced the metagenomes and metatranscriptomes of glucose-amended soil microbial communities in a laboratory incubation.

SUBMITTER: Chuckran PF

PROVIDER: S-EPMC7595945 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil.

Chuckran Peter F PF Huntemann Marcel M Clum Alicia A Foster Brian B Foster Bryce B Roux Simon S Palaniappan Krishnaveni K Varghese Neha N Mukherjee Supratim S Reddy T B K TBK Daum Chris C Copeland Alex A Ivanova Natalia N NN Kyrpides Nikos C NC Del Rio Tijana Glavina TG Eloe-Fadrosh Emiley A EA Morrissey Ember M EM Schwartz Egbert E Fofanov Viacheslav V Hungate Bruce B Dijkstra Paul P

Microbiology resource announcements 20201029 44

The addition of glucose to soil has long been used to study the metabolic activity of microbes in soil; however, the response of the microbial ecophysiology remains poorly characterized. To address this, we sequenced the metagenomes and metatranscriptomes of glucose-amended soil microbial communities in a laboratory incubation. ...[more]

PMID: 33122409

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Project description:Here, we report on the construction of a metagenomic library from a chitin-amended disease-suppressive agricultural soil and its screening for genes that encode novel chitinolytic enzymes. The library, constructed in fosmids in an Escherichia coli host, comprised 145,000 clones containing inserts of sizes of 21 to 40 kb, yielding a total of approximately 5.8 GB of cloned soil DNA. Using genetic screenings by repeated PCR cycles aimed to detect gene sequences of the bacterial chitinase A-class (hereby named chi A genes), we identified and characterized five fosmids carrying candidate genes for chitinolytic enzymes. The analysis thus allowed access to the genomic (fosmid-borne) context of these genes. Using the chiA-targeted PCR, which is based on degenerate primers, the five fosmids all produced amplicons, of which the sequences were related to predicted chitinolytic enzyme-encoding genes of four different host organisms, including Stenotrophomonas maltophilia. Sequencing and de novo annotation of the fosmid inserts confirmed that each one of these carried one or more open reading frames that were predicted to encode enzymes active on chitin, including one for a chitin deacetylase. Moreover, the genetic contexts in which the putative chitinolytic enzyme-encoding genes were located were unique per fosmid. Specifically, inserts from organisms related to Burkholderia sp., Acidobacterium sp., Aeromonas veronii, and the chloroflexi Nitrolancetus hollandicus and/or Ktedonobacter racemifer were obtained. Remarkably, the S. maltophilia chiA-like gene was found to occur in two different genetic contexts (related to N. hollandicus/K. racemifer), indicating the historical occurrence of genetic reshufflings in this part of the soil microbiota. One fosmid containing the insert composed of DNA from the N. hollandicus-like organism (denoted 53D1) was selected for further work. Using subcloning procedures, its putative gene for a chitinolytic enzyme was successfully brought to expression in an E. coli host. On the basis of purified protein preparations, the produced protein was characterized as a chitobiosidase of 43.6 kDa, with a pI of 4.83. Given its activity spectrum, it can be typified as a halotolerant chitobiosidase.

Dataset Information

Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil.

Publications

Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil.

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