Aquatic ecosystems are globally significant sources of the greenhouse gas methane to the atmosphere. Until recently, methane production was thought to be a strictly anaerobic process confined ...primarily to anoxic sediments. However, supersaturation of methane in oxygenated waters has been consistently observed in lakes and the ocean (termed the 'methane paradox'), indicating that methane can be produced under oxic conditions through unclear mechanisms. Here we show aerobic methane production from multiple sources in freshwater incubation experiments under different treatments and based on biogeochemical, metagenomic, and metatranscriptomic data. We find that aerobic methane production appears to be associated with (bacterio)chlorophyll metabolism and photosynthesis, as well as with Proteobacterial degradation of methylphosphonate. Genes encoding pathways for putative photosynthetic- and methylphosphonate-based methane production also co-occur in Proteobacterial metagenome-assembled genomes. Our findings provide insight into known mechanisms of aerobic methane production, and suggest a potential co-occurring mechanism associated with bacterial photosynthesis in aquatic ecosystems.
Biological productivity in most of the world's oceans is controlled by the supply of nutrients to surface waters. The relative balance between supply and removal of nutrientsincluding nitrogen, iron ...and phosphorusdetermines which nutrient limits phytoplankton growth. Although nitrogen limits productivity in much of the ocean, large portions of the tropics and subtropics are defined by extreme nitrogen depletion. In these regions, microbial denitrification removes biologically available forms of nitrogen from the water column, producing substantial deficits relative to other nutrients. Here we demonstrate that nitrogen-deficient areas of the tropical and subtropical oceans are acutely vulnerable to nitrogen pollution. Despite naturally high nutrient concentrations and productivity, nitrogen-rich agricultural runoff fuels large (54-577 km2) phytoplankton blooms in the Gulf of California. Runoff exerts a strong and consistent influence on biological processes, in 80% of cases stimulating blooms within days of fertilization and irrigation of agricultural fields. We project that by the year 2050, 27-59% of all nitrogen fertilizer will be applied in developing regions located upstream of nitrogen-deficient marine ecosystems. Our findings highlight the present and future vulnerability of these ecosystems to agricultural runoff.
Summary
Microbial communities are key components of lake ecosystems and play central roles in lake biogeochemical cycles. Freshwater lakes, in turn, have a disproportionate influence on global carbon ...and nitrogen cycling, while also acting as ‘sentinels’ of environmental change. Determining what factors regulate microbial community dynamics and their relationship to lake biogeochemistry is therefore essential to understanding global change feedbacks. We used Illumina sequencing of >2 million 16S rRNA genes to examine microbial community structure and diversity in relation to spatial, temporal and biogeochemical variation, within and across lakes located along a 871 m elevation gradient in Yosemite National Park, California, USA. We captured a rich microbial community that included many rare operational taxonomic units (OTUs), but was dominated by a few bacterial classes and OTUs frequently detected in other freshwater ecosystems. Neither richness, evenness nor overall diversity was directly related to elevation. However, redundancy analysis showed that changes in microbial community structure were significantly related to elevation. Along with sampling period and dissolved nutrient concentrations, 29% of the variation in community structure could be explained by measured variables – in congruence with studies in other lakes using different techniques. We also found a distance–decay relationship in microbial community structure across lakes, suggesting that both local environmental factors and dispersal play a role in structuring communities.
Long-term declines in oxygen concentrations are evident throughout much of the ocean interior and are particularly acute in midwater oxygen minimum zones (OMZs). These regions are defined by ...extremely low oxygen concentrations (<20-45 μmol kg(-1)), cover wide expanses of the ocean, and are associated with productive oceanic and coastal regions. OMZs have expanded over the past 50 years, and this expansion is predicted to continue as the climate warms worldwide. Shoaling of the upper boundaries of the OMZs accompanies OMZ expansion, and decreased oxygen at shallower depths can affect all marine organisms through multiple direct and indirect mechanisms. Effects include altered microbial processes that produce and consume key nutrients and gases, changes in predator-prey dynamics, and shifts in the abundance and accessibility of commercially fished species. Although many species will be negatively affected by these effects, others may expand their range or exploit new niches. OMZ shoaling is thus likely to have major and far-reaching consequences.
Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, occurs in a wide variety of environments and plays a central role in the global nitrogen cycle. Catalyzed by the enzyme ...ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the β- and γ-Proteobacteria. However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase α-subunit (amoA) genes derived from uncultivated, nonextremophilic Crenarchaeota. Here, we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. Using PCR primers designed to specifically target archaeal amoA, we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. Diverse and distinct AOA communities are associated with each of these habitats, with little overlap between water columns and sediments. Within marine sediments, most AOA sequences are unique to individual sampling locations, whereas a small number of sequences are evidently cosmopolitan in distribution. Considering the abundance of non-extremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle.
Microbial communities control numerous biogeochemical processes critical for ecosystem function and health. Most analyses of coastal microbial communities focus on the characterization of bacteria ...present in either sediment or seawater, with fewer studies characterizing both sediment and seawater together at a given site, and even fewer studies including information about non-bacterial microbial communities. As a result, knowledge about the ecological patterns of microbial biodiversity across domains and habitats in coastal communities is limited-despite the fact that archaea, bacteria, and microbial eukaryotes are present and known to interact in coastal habitats. To better understand microbial biodiversity patterns in coastal ecosystems, we characterized sediment and seawater microbial communities for three sites along the coastline of Puerto Nuevo, Baja California, Mexico using both 16S and 18S rRNA gene amplicon sequencing. We found that sediment hosted approximately 500-fold more operational taxonomic units (OTUs) for bacteria, archaea, and microbial eukaryotes than seawater (p < 0.001). Distinct phyla were found in sediment versus seawater samples. Of the top ten most abundant classes, Cytophagia (bacterial) and Chromadorea (eukaryal) were specific to the sediment environment, whereas Cyanobacteria and Bacteroidia (bacterial) and Chlorophyceae (eukaryal) were specific to the seawater environment. A total of 47 unique genera were observed to comprise the core taxa community across environment types and sites. No archaeal taxa were observed as part of either the abundant or core taxa. No significant differences were observed for sediment community composition across domains or between sites. For seawater, the bacterial and archaeal community composition was statistically different for the Major Outlet site (p < 0.05), the site closest to a residential area, and the eukaryal community composition was statistically different between all sites (p < 0.05). Our findings highlight the distinct patterns and spatial heterogeneity in microbial communities of a coastal region in Baja California, Mexico.
Ammonia-oxidizing microorganisms compete with phytoplankton for reduced nitrogen in the euphotic zone and provide oxidized nitrogen to other microbes present in the sea. We report 15NH⁺₄ oxidation ...rate measurements made at 5–20-m resolution using an in situ array and quantification of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in corresponding samples from the upper water column and oxygen minimum zone (OMZ) of the Gulf of California (GOC) and eastern tropical North Pacific Ocean (ETNP). 15NH⁺₄ oxidation rates varied substantially with depth and between stations: they were greatest at the base of the euphotic zone, and maximum rates were up to 28-fold greater than rates measured within 5–10 m. Pyrosequencing and quantitative polymerase chain reactions (QPCR) indicated that AOA were present throughout the water column at all latitudes and always outnumbered AOB. AOB constituted only 39 of 432,240 16S ribosomal ribonucleic acid gene sequences produced via pyrosequencing but were more abundant at greater depths and higher latitudes. 15NH⁺₄ oxidation rates were correlated with AOA abundance at some stations and were detectable in 96% of samples, including depths where oxygen concentrations were < 5 μmol kg−1 and depths within the euphotic zone, where up to 42% of ammonia oxidation occurred. Ammonia is rapidly oxidized within discrete depth intervals in the GOC and ETNP; while pyrosequencing and QPCR demonstrate that AOB are confined to deeper portions of the water column, AOA appear to be active within the euphotic zone, where they may quickly respond to nitrogen inputs.
Ocean acidification produced by dissolution of anthropogenic carbon dioxide (CO₂) emissions in seawater has profound consequences for marine ecology and biogeochemistry. The oceans have absorbed ...one-third of CO₂ emissions over the past two centuries, altering ocean chemistry, reducing seawater pH, and affecting marine animals and phytoplankton in multiple ways. Microbially mediated ocean biogeochemical processes will be pivotal in determining how the earth system responds to global environmental change; however, how they may be altered by ocean acidification is largely unknown. We show here that microbial nitrification rates decreased in every instance when pH was experimentally reduced (by 0.05-0.14) at multiple locations in the Atlantic and Pacific Oceans. Nitrification is a central process in the nitrogen cycle that produces both the greenhouse gas nitrous oxide and oxidized forms of nitrogen used by phytoplankton and other microorganisms in the sea; at the Bermuda Atlantic Time Series and Hawaii Ocean Time-series sites, experimental acidification decreased ammonia oxidation rates by 38% and 36%. Ammonia oxidation rates were also strongly and inversely correlated with pH along a gradient produced in the oligotrophic Sargasso Sea (r² = 0.87, P < 0.05). Across all experiments, rates declined by 8-38% in low pH treatments, and the greatest absolute decrease occurred where rates were highest off the California coast. Collectively our results suggest that ocean acidification could reduce nitrification rates by 3-44% within the next few decades, affecting oceanic nitrous oxide production, reducing supplies of oxidized nitrogen in the upper layers of the ocean, and fundamentally altering nitrogen cycling in the sea.
Oceanic oxygen minimum zones (OMZs) have a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that ...control these cycles is unclear. Here we sample across dissolved oxygen gradients in the oceans' largest OMZ and show that bacterial richness displays a unimodal pattern with decreasing dissolved oxygen, reaching maximum values on the edge of the OMZ and decreasing within it. Rare groups on the OMZ margin are abundant at lower dissolved oxygen concentrations, including sulphur-cycling Chromatiales, for which 16S rRNA was amplified from extracted RNA. Microbial species distribution models accurately replicate community patterns based on multivariate environmental data, demonstrate likely changes in distributions and diversity in the eastern tropical North Pacific Ocean, and highlight the sensitivity of key bacterial groups to deoxygenation. Through these mechanisms, OMZ expansion may alter microbial composition, competition, diversity and function, all of which have implications for biogeochemical cycling in OMZs.
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