scholarly journals Freshwater carbon and nutrient cycles revealed through reconstructed population genomes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6075 ◽  
Author(s):  
Alexandra M. Linz ◽  
Shaomei He ◽  
Sarah L.R. Stevens ◽  
Karthik Anantharaman ◽  
Robin R. Rohwer ◽  
...  
Keyword(s):  
Time Series ◽  
Nitrogen Fixation ◽  
Carbon Fixation ◽  
Lake Trout ◽  
Biogeochemical Cycling ◽  
Eutrophic Lake ◽  
Glycoside Hydrolases ◽  
Dissimilatory Sulfate Reduction ◽  
Hydrogen Metabolism ◽  
Lake Mendota

Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.

scholarly journals Connections between freshwater carbon and nutrient cycles revealed through reconstructed population genomes

2018 ◽  
Author(s):  
Alexandra M. Linz ◽  
Shaomei He ◽  
Sarah L. R. Stevens ◽  
Karthik Anantharaman ◽  
Robin R. Rohwer ◽  
...  
Keyword(s):  
Time Series ◽  
Nitrogen Fixation ◽  
Nutrient Cycling ◽  
Marker Gene ◽  
Functional Marker ◽  
Glycoside Hydrolases ◽  
Marker Genes ◽  
Nutrient Cycles ◽  
Lake Mendota ◽  
Genes Encoding

AbstractMetabolic processes at the microbial scale influence ecosystem functions because microbes are responsible for much of the carbon and nutrient cycling in freshwater. One approach to predict the metabolic capabilities of microbial communities is to search for functional marker genes in metagenomes. However, this approach does not provide context about co-occurrence with other metabolic traits within an organism or detailed taxonomy about those organisms. Here, we combine a functional marker gene analysis with metabolic pathway prediction of microbial population genomes (MAGs) assembled from metagenomic time series in eutrophic Lake Mendota and humic Trout Bog to identify how carbon and nutrient cycles are connected in freshwater. We found that phototrophy, carbon fixation, and nitrogen fixation pathways co-occurred in Cyanobacteria MAGs in Lake Mendota and in Chlorobiales MAGs in Trout Bog. Cyanobacteria MAGs also had strong temporal correlations to functional marker genes for nitrogen fixation in several years. Genes encoding steps in the nitrogen and sulfur cycles varied in abundance and taxonomy by lake, potentially reflecting the availability and composition of inorganic nutrients in these systems. We were also able to identify which populations contained the greatest density and diversity of genes encoding glycoside hydrolases. Populations with many glycoside hydrolases also encoded pathways for sugar degradation. By using both MAGs and marker genes, we were better able to link functions to specific taxonomic groups in our metagenomic time series, enabling a more detailed understanding of freshwater microbial carbon and nutrient cycling.

scholarly journals The Role of Nitrogen Fixation in Cyanobacterial Bloom Toxicity in a Temperate, Eutrophic Lake

PLoS ONE ◽  
2013 ◽  
Vol 8 (2) ◽  
pp. e56103 ◽  
Author(s):  
Lucas J. Beversdorf ◽  
Todd R. Miller ◽  
Katherine D. McMahon
Keyword(s):  
Nitrogen Fixation ◽  
Cyanobacterial Bloom ◽  
Eutrophic Lake

scholarly journals Cryptic oxygen cycling in anoxic marine zones

2017 ◽  
Vol 114 (31) ◽  
pp. 8319-8324 ◽  
Author(s):  
Emilio Garcia-Robledo ◽  
Cory C. Padilla ◽  
Montserrat Aldunate ◽  
Frank J. Stewart ◽  
Osvaldo Ulloa ◽  
...  
Keyword(s):  
Surface Layer ◽  
Carbon Fixation ◽  
Nitrogen Loss ◽  
Biogeochemical Cycling ◽  
Oxygenic Photosynthesis ◽  
Nitrite Oxidation ◽  
Tight Coupling ◽  
Expression Of Genes ◽  
Aerobic Processes ◽  
Oxygen Cycling

Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30–50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteriaProchlorococcusspp. Free O2levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.

scholarly journals Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling

2017 ◽  
Vol 84 (1) ◽  
Author(s):  
Michael D. Lee ◽  
Eric A. Webb ◽  
Nathan G. Walworth ◽  
Fei-Xue Fu ◽  
Noelle A. Held ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Carbon Fixation ◽  
Community Respiration ◽  
Ecological Niches ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Globally Distributed

ABSTRACTTrichodesmiumis a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs,Trichodesmiumserves as a host to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here, we utilized metatranscriptomics to examine gene expression activities of microbial communities associated withTrichodesmium erythraeum(strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor microbial communities similar to those of natural populations. In enrichments maintained under two distinct CO2concentrations for ∼8 years, the community transcriptional profiles were found to be specific to the treatment, demonstrating a restructuring of overall gene expression had occurred. Some of this restructuring involved significant increases in community respiration-related transcripts under elevated CO2, potentially facilitating the corresponding measured increases in host nitrogen fixation rates. Particularly of note, in both treatments, community transcripts involved in the reduction of nitrate, nitrite, and nitrous oxide were detected, suggesting the associated organisms may play a role in colony-level nitrogen cycling. Lastly, a taxon-specific analysis revealed distinct ecological niches of consistently cooccurring major taxa that may enable, or even encourage, the stable cohabitation of a diverse community withinTrichodesmiumconsortia.IMPORTANCETrichodesmiumis a genus of globally distributed, nitrogen-fixing marine cyanobacteria. As a source of new nitrogen in otherwise nitrogen-deficient systems, these organisms help fuel carbon fixation carried out by other more abundant photoautotrophs and thereby have significant roles in global nitrogen and carbon cycling. Members of theTrichodesmiumgenus tend to form large macroscopic colonies that appear to perpetually host an association of diverse interacting microbes distinct from the surrounding seawater, potentially making the entire assemblage a unique miniature ecosystem. Since its first successful cultivation in the early 1990s, there have been questions about the potential interdependencies betweenTrichodesmiumand its associated microbial community and whether the host's seemingly enigmatic nitrogen fixation schema somehow involved or benefited from its epibionts. Here, we revisit these old questions with new technology and investigate gene expression activities of microbial communities living in association withTrichodesmium.

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