Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs in deep sea cold seep sediments. However, it is unclear whether other microbial groups can perform nitrogen fixation in such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, and six metatranscriptomes derived from 11 globally distributed cold seeps. These sediments contain phylogenetically diverse nitrogenase genes corresponding to an expanded diversity of diazotrophic lineages. Diverse catabolic pathways were predicted to provide ATP for nitrogen fixation, suggesting diazotrophy in cold seeps is not necessarily associated with sulfate-dependent anaerobic oxidation of methane. Nitrogen fixation genes among various diazotrophic groups in cold seeps were inferred to be genetically mobile and subject to purifying selection. Our findings extend the capacity for diazotrophy to five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota and UBA6262), and suggest that cold seep diazotrophs might contribute substantially to the global nitrogen balance.
The
rapid emergence of antibiotic resistance genes (ARGs) has become
an increasingly serious threat to public health. Previous studies
illustrate the antibiotic-like effect of many substances. However,
whether and how commonly used or existing non-antibiotic metalloids
(e.g., selenate) would enhance ARG spread remains poorly known. Here,
we tracked the long-term operation of a bioreactor continuously fed
with selenate for more than 1000 days. Metagenomic sequencing identified
191 different ARGs, of which the total abundance increased significantly
after the amendment of selenate. Network analyses showed that ARGs
resisting multiple drugs had very similar co-occurrence patterns,
implying a potentially larger health risk. Host classification not
only indicated multidrug-resistant species but also distinguished
the mechanism of ARG enrichment for vertical transfer and horizontal
gene transfer. Genome reconstruction of an ARG host suggested that
selenate and its bioreduction product selenite could stimulate the
overproduction of intracellular reactive oxygen species, which was
confirmed by the direct measurement. Bacterial membrane permeability,
type IV pilus formation, and DNA repair and recombination were also
enhanced, together facilitating the horizontal acquirement of ARGs.
Overall, this study for the first time highlights the ARG emergence
and dissemination induced by a non-antibiotic metalloid and identifies
ARG as a factor to consider in selenate bioremediation.
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