Identification, mutagenesis, and transcriptional analysis of the methanesulfonate transport operon of Methylosulfonomonas methylovora

North Sea spring bloom-associated Gammaproteobacteria fill diverse heterotrophic niches

BACKGROUND

The planktonic bacterial community associated with spring phytoplankton blooms in the North Sea is responsible for a large amount of carbon turnover in an environment characterised by high primary productivity. Individual clades belonging to the Gammaproteobacteria have shown similar population dynamics to Bacteroidetes species, and are thus assumed to fill competing ecological niches. Previous studies have generated large numbers of metagenome assembled genomes and metaproteomes from these environments, which can be readily mined to identify populations performing potentially important ecosystem functions. In this study we attempt to catalogue these spring bloom-associated Gammaproteobacteria, which have thus far attracted less attention than sympatric Alphaproteobacteria and Bacteroidetes.

METHODS

We annotated 120 non-redundant species-representative gammaproteobacterial metagenome assembled genomes from spring bloom sampling campaigns covering the four years 2010-2012 and 2016 using a combination of Prokka and PfamScan, with further confirmation via BLAST against NCBI-NR. We also matched these gene annotations to 20 previously published metaproteomes covering those sampling periods plus the spring of 2009.

RESULTS

Metagenome assembled genomes with clear capacity for polysaccharide degradation via dedicated clusters of carbohydrate active enzymes were among the most abundant during blooms. Many genomes lacked gene clusters with clearly identifiable predicted polysaccharide substrates, although abundantly expressed loci for the uptake of large molecules were identified in metaproteomes. While the larger biopolymers, which are the most abundant sources of reduced carbon following algal blooms, are likely the main energy source, some gammaproteobacterial clades were clearly specialised for smaller organic compounds. Their substrates range from amino acids, monosaccharides, and DMSP, to the less expected, such as terpenoids, and aromatics and biphenyls, as well as many 'unknowns'. In particular we uncover a much greater breadth of apparent methylotrophic capability than heretofore identified, present in several order level clades without cultivated representatives.

CONCLUSIONS

Large numbers of metagenome assembled genomes are today publicly available, containing a wealth of readily accessible information. Here we identified a variety of predicted metabolisms of interest, which include diverse potential heterotrophic niches of spring bloom-associated Gammaproteobacteria. Features such as those identified here could well be fertile ground for future experimental studies.

Isoprene Oxidation by the Gram-Negative Model bacterium Variovorax sp. WS11

Plant-produced isoprene (2-methyl-1,3-butadiene) represents a significant portion of global volatile organic compound production, equaled only by methane. A metabolic pathway for the degradation of isoprene was first described for the Gram-positive bacterium Rhodococcus sp. AD45, and an alternative model organism has yet to be characterised. Here, we report the characterisation of a novel Gram-negative isoprene-degrading bacterium, Variovorax sp. WS11. Isoprene metabolism in this bacterium involves a plasmid-encoded iso metabolic gene cluster which differs from that found in Rhodococcus sp. AD45 in terms of organisation and regulation. Expression of iso metabolic genes is significantly upregulated by both isoprene and epoxyisoprene. The enzyme responsible for the initial oxidation of isoprene, isoprene monooxygenase, oxidises a wide range of alkene substrates in a manner which is strongly influenced by the presence of alkyl side-chains and differs from other well-characterised soluble diiron monooxygenases according to its response to alkyne inhibitors. This study presents Variovorax sp. WS11 as both a comparative and contrasting model organism for the study of isoprene metabolism in bacteria, aiding our understanding of the conservation of this biochemical pathway across diverse ecological niches.

Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment

Methanesulfonic acid (MSA) is a relevant intermediate of the biogeochemical cycle of sulfur and environmental microorganisms assume an important role in the mineralization of this compound. Several methylotrophic bacterial strains able to grow on MSA have been isolated from soil or marine water and two conserved operons, msmABCD coding for MSA monooxygenase and msmEFGH coding for a transport system, have been repeatedly encountered in most of these strains. Homologous sequences have also been amplified directly from the environment or observed in marine metagenomic data, but these showed a base composition (G + C content) very different from their counterparts from cultivated bacteria. The aim of this study was to understand which microorganisms within the coastal surface oceanic microflora responded to MSA as a nutrient and how the community evolved in the early phases of an enrichment by means of metagenome and gene-targeted amplicon sequencing. From the phylogenetic point of view, the community shifted significantly with the disappearance of all signals related to the Archaea, the Pelagibacteraceae and phylum SAR406, and the increase in methylotroph-harboring taxa, accompanied by other groups so far not known to comprise methylotrophs such as the Hyphomonadaceae. At the functional level, the abundance of several genes related to sulfur metabolism and methylotrophy increased during the enrichment and the allelic distribution of gene msmA diagnostic for MSA monooxygenase altered considerably. Even more dramatic was the disappearance of MSA import-related gene msmE, which suggests that alternative transporters must be present in the enriched community and illustrate the inadequacy of msmE as an ecofunctional marker for MSA degradation at sea.

Methanesulfonate (MSA) Catabolic Genes from Marine and Estuarine Bacteria

Quantitatively, methanesulfonate (MSA) is a very relevant compound in the global biogeochemical sulfur cycle. Its utilization by bacteria as a source of carbon and energy has been described and a specific enzyme, methanesulfonate monooxygenase (MSAMO), has been found to perform the first catabolic step of its oxidation. Other proteins seemingly involved in the import of MSA into bacterial cells have been reported. In this study, we obtained novel sequences of genes msmA and msmE from marine, estuary and soil MSA-degraders (encoding the large subunit of the MSAMO enzyme and the periplasmic component of the import system, respectively). We also obtained whole-genome sequences of two novel marine Filomicrobium strains, Y and W, and annotated two full msm operons in these genomes. Furthermore, msmA and msmE sequences were amplified from North Atlantic seawater and analyzed. Good conservation of the MsmA deduced protein sequence was observed in both cultured strains and metagenomic clones. A long spacer sequence in the Rieske-type [2Fe-2S] cluster-binding motif within MsmA was found to be conserved in all instances, supporting the hypothesis that this feature is specific to the large (α) subunit of the MSAMO enzyme. The msmE gene was more difficult to amplify, from both cultivated isolates and marine metagenomic DNA. However, 3 novel msmE sequences were obtained from isolated strains and one directly from seawater. With both genes, our results combined with previous metagenomic analyses seem to imply that moderate to high-GC strains are somehow favored during enrichment and isolation of MSA-utilizing bacteria, while the majority of msm genes obtained by cultivation-independent methods have low levels of GC%, which is a clear example of the misrepresentation of natural populations that culturing, more often than not, entails. Nevertheless, the data obtained in this work show that MSA-degrading bacteria are abundant in surface seawater, which suggests ecological relevance for this metabolic group of bacteria.

Complete Genome Sequences of Two Strains of "Candidatus Filomicrobium marinum," a Methanesulfonate-Degrading Species

Two novel methanesulfonate-degrading bacterial strains of “Candidatus Filomicrobium marinum” (strains Y and W) were isolated from a marine water enrichment, and their complete genome sequences are presented here. These are the first full genomes reported for the genus Filomicrobium and for methanesulfonate (MSA)-degrading bacteria.

Characterization of a novel Rieske-type alkane monooxygenase system in Pusillimonas sp. strain T7-7

The cold-tolerant bacterium Pusillimonas sp. strain T7-7 is able to utilize diesel oils (C5 to C30 alkanes) as a sole carbon and energy source. In the present study, bioinformatics, proteomics, and real-time reverse transcriptase PCR approaches were used to identify the alkane hydroxylation system present in this bacterium. This system is composed of a Rieske-type monooxygenase, a ferredoxin, and an NADH-dependent reductase. The function of the monooxygenase, which consists of one large (46.711 kDa) and one small (15.355 kDa) subunit, was further studied using in vitro biochemical analysis and in vivo heterologous functional complementation tests. The purified large subunit of the monooxygenase was able to oxidize alkanes ranging from pentane (C5) to tetracosane (C24) using NADH as a cofactor, with greatest activity on the C15 substrate. The large subunit also showed activity on several alkane derivatives, including nitromethane and methane sulfonic acid, but it did not act on any aromatic hydrocarbons. The optimal reaction condition of the large subunit is pH 7.5 at 30°C. Fe(2+) can enhance the activity of the enzyme evidently. This is the first time that an alkane monooxygenase system belonging to the Rieske non-heme iron oxygenase family has been identified in a bacterium.

Expression patterns reveal niche diversification in a marine microbial assemblage

Resolving the ecological niches of coexisting marine microbial taxa is challenging due to the high species richness of microbial communities and the apparent functional redundancy in bacterial genomes and metagenomes. Here, we generated over 11 million Illumina reads of protein-encoding transcripts collected from well-mixed southeastern US coastal waters to characterize gene expression patterns distinguishing the ecological roles of hundreds of microbial taxa sharing the same environment. The taxa with highest in situ growth rates (based on relative abundance of ribosomal protein transcripts) were typically not the greatest contributors to community transcription, suggesting strong top-down ecological control, and their diverse transcriptomes indicated roles as metabolic generalists. The taxa with low in situ growth rates typically had low diversity transcriptomes dominated by specialized metabolisms. By identifying protein-encoding genes with atypically high expression for their level of conservation, unique functional roles of community members emerged related to substrate use (such as complex carbohydrates, fatty acids, methanesulfonate, taurine, tartrate, ectoine), alternative energy-conservation strategies (proteorhodopsin, AAnP, V-type pyrophosphatases, sulfur oxidation, hydrogen oxidation) and mechanisms for negotiating a heterogeneous environment (flagellar motility, gliding motility, adhesion strategies). On average, the heterotrophic bacterioplankton dedicated 7% of their transcriptomes to obtaining energy by non-heterotrophic means. This deep sequencing of a coastal bacterioplankton transcriptome provides the most highly resolved view of bacterioplankton niche dimensions yet available, uncovering a spectrum of unrecognized ecological strategies.

Microbial degradation of dimethylsulphide and related C1-sulphur compounds: organisms and pathways controlling fluxes of sulphur in the biosphere

Dimethylsulphide (DMS) plays a major role in the global sulphur cycle. It has important implications for atmospheric chemistry, climate regulation, and sulphur transport from the marine to the atmospheric and terrestrial environments. In addition, DMS acts as an info-chemical for a wide range of organisms ranging from micro-organisms to mammals. Micro-organisms that cycle DMS are widely distributed in a range of environments, for instance, oxic and anoxic marine, freshwater and terrestrial habitats. Despite the importance of DMS that has been unearthed by many studies since the early 1970s, the understanding of the biochemistry, genetics, and ecology of DMS-degrading micro-organisms is still limited. This review examines current knowledge on the microbial cycling of DMS and points out areas for future research that should shed more light on the role of organisms degrading DMS and related compounds in the biosphere.

Identification of two vicinal operons for the degradation of 2-aminobenzenesulfonate encoded on plasmid pSAH in Alcaligenes sp. strain O-1

Alcaligenes sp. strain O-1 inducibly deaminates 2-aminobenzenesulfonate (ABS) via dioxygenation to 3-sulfocatechol, which is desulfonated during meta ring-cleavage to yield 2-hydroxymuconate. This intermediate is transformed through the oxalocrotonate-branch of the sulfocatechol meta-pathway (Scm). The complete pathway is encoded on the 180-kb plasmid pSAH, 20kb of which was sequenced. Twenty open reading frames (ORFs) were detected. Two clusters (abs and scm) with degradative genes were surrounded by several transposon-related ORFs. The six genes of the abs cluster were shown to be co-transcribed, and contained the genes for two characterised subunits of the oxygenase component of the ABS-dioxygenase system, and genes putatively encoding ABS-transport functions with similarities to (a) an ABC-type transporter system and (b) a putative major facilitator superfamily transporter. No gene encoding the reductase for the oxygenase system was present in the abs gene cluster, but a candidate gene was found in the scm cluster. The seven-gene scm cluster was also transcribed as single polycistronic message. Functions could be attributed to the gene products, but one enzyme, which was shown to be present, 2-hydroxymuconate isomerase, was not encoded in the scm cluster. No transcriptional regulator was found. This genetic information on the degradation of ABS in strain O-1 provides another example of both split operons and dispersed pathway genes.

Evidence of methanesulfonate utilizers in the Sargasso Sea metagenome

Methanesulfonate (MSA) is one of the products of the photo-oxidation of dimethylsulfide in the atmosphere. The genes responsible for the import of MSA into the cell (msm EFGH) and for its oxidation to formaldehyde (msm ABCD) have been previously sequenced from the soil bacterium Methylosulfonomonas methylovora str. M2 while genes for an MSA monooxygenase have been sequenced from marine bacterium Marinosulfonomonas methylotropha str. TR3. We performed a sequence-based screening of the Sargasso Sea metagenome for homologues of the MSA monooxygenase (MSAMO) and MSA import genes. Our search retrieved one scaffold bearing genes with high identity to the msm ABCD cluster plus two scaffolds bearing genes highly identical to the msm EFGH operon. We increased the available data by sequencing two metagenome plasmids, which revealed more msm genes. In these three cases synteny with the original msm operons was revealed. We also retrieved several singletons showing high identity to shorter segments of the msm clusters or individual msm genes. Furthermore, a characteristic 26-aa internal spacer of the MsmA Rieske-type motif was conserved. Our findings support the case for a significant role of MSA degraders in the marine sulfur cycle and seem to suggest that they may be prominent members of the methylotrophic community in surface ocean waters.