The bacterial endosymbiont of the deep-sea tube worm Riftia pachyptila has never been successfully cultivated outside its host. In the absence of cultivation data we have taken a proteomic approach based on the metagenome sequence to study the metabolism of this peculiar microorganism in detail. As one result, we found that three major sulfide oxidation proteins constitute ~12% of the total cytosolic proteome, highlighting the essential role of these enzymes for the symbiont's energy metabolism.Unexpectedly, the symbiont uses the reductive tricarboxylic acid (TCA) cycle in addition to the previously identified Calvin cycle for CO 2 fixation.
The facultative symbiont of Riftia pachyptila, named here Candidatus Endoriftia persephone, has evaded culture to date, but much has been learned regarding this symbiosis over the past three decades since its discovery. The symbiont population metagenome was sequenced in order to gain insight into its physiology. The population genome indicates that the symbionts use a partial Calvin-Benson Cycle for carbon fixation and the reverse TCA cycle (an alternative pathway for carbon fixation) that contains an unusual ATP citrate lyase. The presence of all genes necessary for heterotrophic metabolism, a phosphotransferase system, and dicarboxylate and ABC transporters indicate that the symbiont can live mixotrophically. The metagenome has a large suite of signal transduction, defence (both biological and environmental) and chemotaxis mechanisms. The physiology of Candidatus Endoriftia persephone is explored with respect to functionality while associated with a eukaryotic host, versus free-living in the hydrothermal environment.
Environmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDNA metabarcoding of COI (cytochrome c oxidase subunit I) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. Finally, our eDNA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDNA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.
Nitrogen-fixing microorganisms (diazotrophs) are keystone species that reduce atmospheric dinitrogen (N 2 ) gas to fixed nitrogen (N), thereby accounting for much of N-based new production annually in the oligotrophic North Pacific. However, current approaches to study N 2 fixation provide relatively limited spatiotemporal sampling resolution; hence, little is known about the ecological controls on these microorganisms or the scales over which they change. In the present study, we used a drifting robotic gene sensor to obtain high-resolution data on the distributions and abundances of N 2 -fixing populations over small spatiotemporal scales. The resulting measurements demonstrate that concentrations of N 2 fixers can be highly variable, changing in abundance by nearly three orders of magnitude in less than 2 days and 30 km. Concurrent shipboard measurements and long-term time-series sampling uncovered a striking and previously unrecognized correlation between phosphate, which is undergoing long-term change in the region, and N 2 -fixing cyanobacterial abundances. These results underscore the value of high-resolution sampling and its applications for modeling the effects of global change.
Nitrogen (N) is the major limiting nutrient for phytoplankton growth and productivity in large parts of the world's oceans. Differential preferences for specific N substrates may be important in controlling phytoplankton community composition. To date, there is limited information on how specific N substrates influence the composition of naturally occurring microbial communities. We investigated the effect of nitrate ( NO3−), ammonium ( NH4+), and urea on microbial and phytoplankton community composition (cell abundances and 16S rRNA gene profiling) and functioning (photosynthetic activity, carbon fixation rates) in the oligotrophic waters of the North Pacific Ocean. All N substrates tested significantly stimulated phytoplankton growth and productivity. Urea resulted in the greatest (>300%) increases in chlorophyll a (<0.06 μg L−1 and ∼0.19 μg L−1 in the control and urea addition, respectively) and productivity (<0.4 μmol C L−1 d−1 and ∼1.4 μmol C L−1 d−1 in the control and urea addition, respectively) at two experimental stations, largely due to increased abundances of Prochlorococcus (Cyanobacteria). Two abundant clades of Prochlorococcus, High Light I and II, demonstrated similar responses to urea, suggesting this substrate is likely an important N source for natural Prochlorococcus populations. In contrast, the heterotrophic community composition changed most in response to NH4+. Finally, the time and magnitude of response to N amendments varied with geographic location, likely due to differences in microbial community composition and their nutrient status. Our results provide support for the hypothesis that changes in N supply would likely favor specific populations of phytoplankton in different oceanic regions and thus, affect both biogeochemical cycles and ecological processes.
32Environmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, 33 principally because they are sensitive and can provide high resolution community composition 34 data. Despite considerable progress in recent years, eDNA studies examining how different 35 environmental sample types can affect species detectability remain rare. Comparisons of 36 environmental samples are especially important for providing best practice guidance on early 37 detection and subsequent mitigation of non-indigenous species. Here we used eDNA 38 metabarcoding of COI (cytochrome c oxidase subunit I) and 18S (nuclear small subunit 39 ribosomal DNA) genes to compare community composition between sediment and water samples 40in artificial coastal sites across the United Kingdom. We first detected markedly different 41 communities and a consistently greater number of distinct operational taxonomic units in 42 sediment compared to water. We then compared our eDNA datasets with previously published 43 rapid assessment biodiversity surveys and found excellent concordance among the different 44 survey techniques. Finally, our eDNA surveys detected many non-indigenous species, including 45 several newly introduced species, highlighting the utility of eDNA metabarcoding for both early 46 detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful 47 consideration on environmental sample type is needed when conducting eDNA surveys, 48 especially for studies assessing community change. 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63Anthropogenic activities have widespread impacts on global biodiversity 1,2 and can negatively 64 affect ecosystem services and function 3 . Cumulatively these actions create an urgent need to 65 develop monitoring tools that rapidly and accurately detect community composition in 66 ecosystems. Existing biodiversity survey techniques have been criticised for their methodological 67 limitations (e.g. observer bias or taxonomic resolution) 4,5 and are typically standardised by a 68 survey time limit or through reaching asymptote of a species discovery curve 6,7 . Such surveys 69 often focus on the detection of a specific taxonomic group that are being targeted, with no ability 70 to retrospectively separate mis-identified species in light of new species discoveries. This is of 71 critical importance for biodiversity monitoring as an increasing number of studies are revealing 72 the widespread presence of molecular cryptic species (i.e. morphologically similar but 73 genetically distinct species 8 ). For example, between 9,000-35,000 marine species (2.7% of the 74 total number of known marine species) are considered molecular cryptic, and genetic studies 75 often reveal widespread marine species containing multiple cryptic lineages 9,10 . This highlights 76 the need to integrate morphological and genetic approaches to accurately detect community 77 composition. 78One approach that has the potential to overcome some of the above limitations is the use of 79 nuclei...
Aquatic microbial communities are central to biogeochemical processes that maintain Earth's habitability. However, there is a significant paucity of data collected from these species in their natural environment. To address this, a suite of ocean-deployable sampling and sensing instrumentation has been developed to retrieve, archive and analyse water samples and their microbial fraction using state of the art genetic assays. Recent deployments have shed new light onto the role microbes play in essential ocean processes and highlight the risks they may pose to coastal populations. Although current designs are generally too large, complex and expensive for widespread use, a host of emerging bio-analytical technologies have the potential to revolutionise this field and open new possibilities in aquatic microbial metrology.
The 'bacterial switch' is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate (DMSP) to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere. Yet which ecological or physiological factors might control the bacterial switch remains a topic of considerable debate. Here we report the first field observations of dynamic changes in expression of DMSP pathway genes by a single marine bacterial species in its natural environment. Detection of taxon-specific gene expression in Roseobacter species HTCC2255 during a month-long deployment of an autonomous ocean sensor in Monterey Bay, CA captured in situ regulation of the first gene in each DMSP pathway (dddP and dmdA) that corresponded with shifts in the taxonomy of the phytoplankton community. Expression of the demethylation pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the cleavage pathway was greater in the presence of a mixed diatom and dinoflagellate community. These field data fit the prevailing hypothesis for bacterial DMSP gene regulation based on bacterial sulfur demand, but also suggest a modification involving oxidative stress response, evidenced as upregulation of catalase via katG, when DMSP is demethylated.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
334 Leonard St
Brooklyn, NY 11211
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.