PXD011642-2

PXD011642 is an original dataset announced via ProteomeXchange.

Title	Competition between microbes during anaerobic oxidation of methane: Bioreactor metaproteomics
Description	In this study, we investigated Mn3+-cycling microbial populations enriched from Lake Matano, Indonesia using metagenomics and metaproteomics. Lake Matano contains an active Mn cycle that links the oxic-anoxic interface with anoxic deep waters that are enriched in iron and manganese, and depleted in sulfate, phosphate, and oxidized nitrogen (Crowe et al., 2008; Jones et al., 2011). Sediments were incubated with sequential transfers for ~1 year with Mn3+ as the sole electron acceptor and methane as organic carbon until achieving sediment-free conditions. Here we investigate this novel species of Dechloromonas (Betaproteobacteria), “Candidatus Dechloromonas occultata,” which was the dominant population in enrichment cultures with active Mn3+ reduction. “Ca. D. occultata” expressed electron conduits related to those involved in Fe2+ oxidation (Mto-like), as well as a novel cytochrome c-rich gene cluster putatively involved in extracellular electron transfer, and an atypical nitrous oxide reductase. According to ribosomal counts, Dechloromonas outnumber Geobacter. In terms of functional genes, Dechloromonas expresses a wider variety and number of genes. Dechloromonas therefore seems to have a (selective?) advantage over Geobacter. Previous experiments revealed that Dechloromonas express nitrogen regulators, reductases and scavenging genes, as well as many carbon central metabolic pathways, and aromatic carbon degradation pathways. Dechloromonas is a beta proteobacteria, and these are "experts" in nitrogen metabolism. Geobacter, on the other hand, is well known for carbon degradation. Our previous experiments lead to our hypothesis that Dechloromonas is more active because they are more successful at acquiring nitrogen, a limiting nutrient for Geobacter. This would further suggest that carbon is not the limiting nutrient. We will test 2 hypotheses with the next suite of experiments 1) pyrophosphate supports the community, by allowing carbon fixation , 2)Dechloromonas has a (selective?) advantage over Geobacter. To test this hypothesis, bioreactors will be used to grow biotriplicate cultures of (1)- CH4 vs. pyrophosphate and (2)-CH4 vs. Mn(III) pyrophosphate. Here we have analyzed whole cell pellets using gas phase fractionations on the Q Exactive. Are Dechloromonas capable of out-competing Geobacter when grown in media with methane as the only carbon source bioreactors because they are capable of acquiring more nitrogen? Source of inoculum. Lake Matano is a metal-rich, ancient ocean analog (Crowe et al. 2011, Jones et al. 2011). Organic carbon in Lake Matano is mostly mineralized via methanogenesis before reaching the iron-rich sediments, limiting organic matter bioavailability for metal-reducers (Kuntz et al. 2015). A 15-cm sediment core from 200 m water depth in Lake Matano, Sulawesi Island, Indonesia (02°26′27.1′′S, 121°15′12.3′′E; in situ sediment temperature ~27°C) was sampled in November 2014 and sub-sampled at 5 cm increments. Sediments were sealed in gas-tight Mylar bags with no headspace (Hansen et al. 2000) and stored at 4°C until incubations began in December 2015.
HostingRepository	PRIDE
AnnounceDate	2020-06-30
AnnouncementXML	Submission_2020-07-05_22:26:23.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Brook Nunn
SpeciesList	scientific name: sediment metagenome; NCBI TaxID: 749907;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-09 03:31:41	ID requested
1	2020-06-29 23:15:53	announced
⏵ 2	2020-07-05 22:26:24	announced	2020-07-06: Updated publication reference for PubMed record(s): 32613749.

Szeinbaum N, Nunn BL, Cavazos AR, Crowe SA, Stewart FJ, DiChristina TJ, Reinhard CT, Glass JB, Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction. Environ Microbiol Rep, 12(5):583-593(2020) [pubmed]

submitter keyword: Lake sediment, bioreactor, Dechloromonas,

Brook L. Nunn
contact affiliation	University of Washington Department of Genome Sciences
contact email	brookh@uw.edu
lab head
Brook Nunn
contact affiliation	University of Washington
contact email	brookh@uw.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011642
     1. Label: PRIDE project
     2. Name: Competition between microbes during anaerobic oxidation of methane: Bioreactor metaproteomics