Background The Mariana Trench is the deepest known site in the Earth’s oceans, reaching a depth of ~ 11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbor distinctive microbial planktonic communities. However, the genetic potential of microbial communities within the hadal zone is poorly understood. Results Here, implementing both culture-dependent and culture-independent methods, we perform extensive analysis of microbial populations and their genetic potential at different depths in the Mariana Trench. Unexpectedly, we observed an abrupt increase in the abundance of hydrocarbon-degrading bacteria at depths > 10,400 m in the Challenger Deep. Indeed, the proportion of hydrocarbon-degrading bacteria at > 10,400 m is the highest observed in any natural environment on Earth. These bacteria were mainly Oleibacter , Thalassolituus , and Alcanivorax genera, all of which include species known to consume aliphatic hydrocarbons. This community shift towards hydrocarbon degraders was accompanied by increased abundance and transcription of genes involved in alkane degradation. Correspondingly, three Alcanivorax species that were isolated from 10,400 m water supplemented with hexadecane were able to efficiently degrade n -alkanes under conditions simulating the deep sea, as did a reference Oleibacter strain cultured at atmospheric pressure. Abundant n- alkanes were observed in sinking particles at 2000, 4000, and 6000 m (averaged 23.5 μg/gdw) and hadal surface sediments at depths of 10,908, 10,909, and 10,911 m (averaged 2.3 μg/gdw). The δ 2 H values of n- C 16/18 alkanes that dominated surface sediments at near 11,000-m depths ranged from − 79 to − 93‰, suggesting that these sedimentary alkanes may have been derived from an unknown heterotrophic source. Conclusions These results reveal that hydrocarbon-degrading microorganisms are present in great abundance in the deepest seawater on Earth and shed a new light on potential biological processes in this extreme environment. Electronic supplementary material The online version of this article (10.1186/s40168-019-0652-3) contains supplementary material, which is available to authorized users.
Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.
BackgroundVibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and environmental adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level.ResultsTwo Vibrio genomes were sequenced and found to occupy many unique orthologues families which absent from the previously genes pool of the complete genomes of vibrios. Comparative genomics analysis found vibrios encompass a steady core-genome and tremendous pan-genome with substantial gene gain and horizontal gene transfer events in the evolutionary history. Evolutionary analysis based on the core-genome tree suggested that V. fischeri emerged ~ 385 million years ago, along with the occurrence of cephalopods and the flourish of fish. The relatively large genomes, the high number of 16S rRNA gene copies, and the presence of R-M systems and CRISPR system help vibrios live in various marine environments. Chitin-degrading related genes are carried in nearly all the Vibrio genomes. The number of chitinase genes in vibrios has been extremely expanded compared to which in the most recent ancestor of the genus. The chitinase A genes were estimated to have evolved along with the genus, and have undergone significant purifying selective force to conserve the ancestral state.ConclusionsVibrios have experienced extremely genome expansion events during their evolutionary history, allowing them to develop various functions to spread globally. Despite their close phylogenetic relationships, vibrios were found to have a tremendous pan-genome with a steady core-genome, which indicates the highly plastic genome of the genus. Additionally, the existence of various chitin-degrading related genes and the expansion of chitinase A in the genus demonstrate the importance of the chitin utilization for vibrios. Defensive systems in the Vibrio genomes may protect them from the invasion of external DNA. These genomic features investigated here provide a better knowledge of how the evolutionary process has forged Vibrio genomes to occupy various niches.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4531-2) contains supplementary material, which is available to authorized users.
Vibrio species are associated with human health and play important roles in the carbon cycle. The interest in the Vibrio ecology in marine pelagic environments has increased in recent years, and the correlations between the Vibrio community structure and various environmental factors have been demonstrated. However, the identification of planktonic Vibrio species and their relationship with particulate matter are unclear. Here, we elucidated the spatiotemporal dynamics of Vibrio diversity and in relation to environmental factors in the northern Chinese marginal seas, which feature complex and ever-changing environmental conditions. Vibrio abundance derived from quantitative PCR analysis was higher in summer (∼1.4 × 106 copies liter−1) than in winter (∼1.9 × 105 copies liter−1). Interestingly, the average amount of free-living (on a 0.22-μm-pore-size filter membrane) Vibrio was higher (∼3.89 times) than that of particle-associated Vibrio (on a 3-μm-pore-size filter membrane), making it likely that the preferential lifestyle of the planktonic Vibrio community was free living. Shifts in Vibrio community composition identified by high-throughput amplicon sequencing of the Vibrio-specific 16S rRNA gene were observed at both spatial and temporal scales, which were mainly driven by temperature, dissolved oxygen, ammonium, salinity, nitrite, and phosphate. The most prominent operational taxonomic units in summer were closely related to Vibrio campbellii and Vibrio caribbeanicus and shifted to those affiliated with Vibrio atlanticus in winter. Our study demonstrated abundant and diverse Vibrio populations in the northern Chinese marginal seas, contributing to a better understanding of their potential ecological roles in these ecosystems. IMPORTANCE The dynamics of Vibrio communities have been shown in many marine habitats that are close to land, including estuary or harbor areas. Here, we investigated the spatiotemporal dynamics of Vibrio populations in the northern Chinese marginal seas, spanning a wide spatial scale. We showed that the abundances of the Vibrio population in the present study were higher than those in most previously studied areas and that Vibrio species are more likely to adopt a free-living lifestyle. Moreover, our results expanded upon previous results by showing a clear shift in the dominant Vibrio species from summer to winter, which was mainly attributable to the reduction in the abundance of dominant species in summer. Overall, this work contributes to the understanding of the ecology of the Vibrio communities in the marginal seas.
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