We investigated methane oxidation in the oxygen minimum zone (OMZ) of the eastern tropical North Pacific (ETNP) off central Mexico. Methane concentrations in the anoxic core of the OMZ reached ~ 20 nmol L−1 at off shelf sites and 34 nmol L−1 at a shelf site. Rates of methane oxidation were determined in ship‐board incubations with 3H‐labeled methane at O2 concentrations 0–75 nmol L−1. In vertical profiles at off‐shelf stations, highest rates were found between the secondary nitrite maximum at ~ 130 m and the methane maximum at 300–400 m in the anoxic core. Methane oxidation was inhibited by addition of 1 μmol L−1 oxygen, which, together with the depth distribution, indicated an anaerobic pathway. A coupling to nitrite reduction was further indicated by the inhibitory effect of the nitric oxide scavenger 2‐phenyl‐4,4,5,5‐tetramethylimidazoline‐1‐oxyl‐3‐oxide (PTIO). Metatranscriptomes from the anoxic OMZ core supported the likely involvement of nitrite‐reducing bacteria of the NC10 clade in anaerobic methane oxidation, but also indicated a potential role for nitrate‐reducing euryarchaeotal methane oxidizers (ANME‐2d). Gammaproteobacteria of the Methanococcales were further detected in both 16S rRNA gene amplicons and metatranscriptomes, but the role of these presumed obligately aerobic methane oxidizers in the anoxic OMZ core is unclear. Given available estimates of water residence time, the measured rates and rate constants (up to ~ 1 yr−1) imply that anaerobic methane oxidation is a substantial methane sink in the ETNP OMZ and hence attenuates the emission of methane from this and possibly other OMZs.

Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for

Although competition, niche partitioning, and spatial isolation have been used to describe the ecology and evolution of macro-organisms, it is less clear to what extent these principles account for the extraordinary levels of bacterial diversity observed in nature. Ecological interactions among bacteria are particularly challenging to address due to methodological limitations and uncertainties over how to recognize fundamental units of diversity and link them to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies. Using a direct challenge assay to investigate inhibitory interactions with members of the bacterial community, we observed a temporal difference in the onset of inhibition. The majority of inhibitory activity exhibited by Salinispora arenicola occurred early in its growth cycle and was linked to antibiotic production. In contrast, most inhibition by Salinispora tropica occurred later in the growth cycle and was more commonly linked to nutrient depletion or other sources. Comparative genomics support these differences, with S. arenicola containing nearly twice the number of secondary metabolite biosynthetic gene clusters as S. tropica, indicating a greater potential for secondary metabolite production. In contrast, S. tropica is enriched in gene clusters associated with the acquisition of growth-limiting nutrients such as iron. Coupled with differences in growth rates, the results reveal that S. arenicola uses interference competition at the expense of growth, whereas S. tropica preferentially employs a strategy of exploitation competition. The results support the ecological divergence of two co-occurring and closely related species of marine bacteria by providing evidence they have evolved fundamentally different strategies to compete in marine sediments.

Next-generation sequencing has increased the coverage of microbial diversity surveys by orders of magnitude, but differentiating artifacts from rare environmental sequences remains a challenge. Clustering 16S rRNA sequences into operational taxonomic units (OTUs) organizes sequence data into groups of 97 % identity, helping to reduce data volumes and avoid analyzing sequencing artifacts by grouping them with real sequences. Here, we analyze sequence abundance distributions across environmental samples and show that 16S rRNA sequences of >99 % identity can represent functionally distinct microorganisms, rendering OTU clustering problematic when the goal is an accurate analysis of organism distribution. Strict postsequencing quality control (QC) filters eliminated the most prevalent artifacts without clustering. Further experiments proved that DNA polymerase errors in polymerase chain reaction (PCR) generate a significant number of substitution errors, most of which pass QC filters. Based on our findings, we recommend minimizing the number of PCR cycles in DNA library preparation and applying strict postsequencing QC filters to reduce the most prevalent artifacts while maintaining a high level of accuracy in diversity estimates. We further recommend correlating rare and abundant sequences across environmental samples, rather than clustering into OTUs, to identify remaining sequence artifacts without losing the resolution afforded by high-throughput sequencing.

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Environmental DNA (eDNA) is an emerging and powerful method for use in marine research, conservation, and management, yet time‐ and resource‐intensive protocols limit the scale of implementation. Long‐range autonomous underwater vehicles equipped with autonomous environmental sample processors (LRAUV‐ESPs) provide a new means for scaling up marine eDNA sample collection and processing. Here, we used eDNA metabarcoding of four marker genes (mitochondrial 12S rRNA, bacterial and archaeal 16S rRNA, nuclear 18S rRNA, and mitochondrial COI), which encompass the diversity of marine species from microbes to vertebrates, to demonstrate the efficacy of an LRAUV‐ESP in sampling eDNA and assessing community structure in the Monterey Bay National Marine Sanctuary. The sequencing results from samples that were autonomously collected were comparable with those collected from a ship at similar locations, times, and depths, supporting previous results that found no significant differences using targeted qPCR. This study demonstrates the potential of equipping autonomous underwater vehicles with ESPs to greatly expand the scale of eDNA sample collection and processing and provide much needed information regarding the changing spatial and temporal patterns of marine biodiversity, especially in many data‐poor regions of the world's oceans.

Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sedimentdwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities.IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.KEYWORDS chemical ecology, marine sediments, microbial communities, secondary metabolites

Marine bacteria are known to produce a wide variety of structurally diverse and biologically active secondary metabolites. Considerably less is known about the ecological functions of these compounds, in part due to methodological challenges associated with this field of research. Here, we review the antagonistic activities mediated by marine bacteria with a focus on activities linked to structurally defined secondary metabolites. Bacterial antagonism has been documented against other marine bacteria as well as eukaryotes, and includes antibiosis, the inhibition of quorum sensing, larval settlement deterrence, and defense against predation. These compounds likely play important ecological roles that ultimately affect ecosystem structure and function, however, much remains to be learned before these roles can be fully appreciated. Recent technological advances coupled with a better understanding of the diverse processes mediated by secondary metabolites provide new opportunities to expand our understanding of the chemical ecology of bacterial antagonism in the marine environment.