Nitrogen cycling in the ocean: new perspectives on processes and paradigms

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach

Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.

Ammonification by kelp associated microbes increases ammonium availability

Microbes contribute biologically available nitrogen to the ocean by fixing nitrogen gas from the atmosphere and by mineralizing organic nitrogen into bioavailable dissolved inorganic nitrogen (DIN). Although the large concentration of plants and algae in marine coastal environments provides ample habitat and reliable resources for microbial communities, the role of the microbiome in host-microbe nitrogen cycling remains poorly understood. We tested whether ammonification by epiphytic microbes increased water column ammonium and improved host access to nitrogen resources by converting organic nitrogen into inorganic nitrogen that is available for assimilation by hosts. When bull kelp (Nereocystis luetkeana) in the northeast Pacific was incubated with 15N labelled amino acid tracers, there was accumulation of 15N in kelp tissue, as well as accumulation of 15NH4 in seawater, all consistent with the conversion of dissolved organic nitrogen to ammonium. Metagenomic analysis of surface microbes from two populations of Nereocystis indicated relative similarity in the percentage of genes related to ammonification between the two locations, though the stressed kelp population that had lower tissue nitrogen and a sparser microbiome had greater ammonification rates. Microbial communities on coastal macrophytes may contribute to the nitrogen requirements of their hosts through metabolisms that make ammonium available.

Effects of intensive chlorine disinfection on nitrogen and phosphorus removal in WWTPs

The increased use of disinfection since the pandemic has led to increased effective chlorine concentration in municipal wastewater. Whereas, the specific impacts of active chlorine on nitrogen and phosphorus removal, the mediating communities, and the related metabolic activities in wastewater treatment plants (WWTPs) lack systematic investigation. We systematically analyzed the influences of chlorine disinfection on nitrogen and phosphorus removal activities using activated sludge from five full-scale WWTPs. Results showed that at an active chlorine concentration of 1.0 mg/g-SS, the nitrogen and phosphorus removal systems were not significantly affected. Major effects were observed at 5.0 mg/g-SS, where the nitrogen and phosphorus removal efficiency decreased by 38.9 % and 44.1 %, respectively. At an active chlorine concentration of 10.0 mg/g-SS, the nitrification, denitrification, phosphorus release and uptake activities decreased by 15.1 %, 69.5-95.9 %, 49.6 % and 100 %, respectively. The proportion of dead cells increased by 6.1 folds. Reverse transcriptional quantitative polymerase chain reaction (RT-qPCR) analysis showed remarkable inhibitions on transcriptions of the nitrite oxidoreductase gene (nxrB), the nitrite reductase genes (nirS and nirK), and the nitrite reductase genes (narG). The nitrogen and phosphorus removal activities completely disappeared with an active chlorine concentration of 25.0 mg/g-SS. Results also showed distinct sensitivities of different functional bacteria in the activated sludge. Even different species within the same functional group differ in their susceptibility. This study provides a reference for the understanding of the threshold active chlorine concentration values which may potentially affect biological nitrogen and phosphorus removal in full-scale WWTPs, which are expected to be beneficial for decision-making in WWTPs to counteract the potential impacts of increased active chlorine concentrations in the influent wastewater.

Temporal patterns and driving factors of sediment carbon, nitrogen, and phosphorus stoichiometry in a eutrophication plateau lake

Stoichiometry determines the key characteristics of organisms and ecosystems on a global scale and provides strong instructions on the fate of sediment carbon, nitrogen, and phosphorus (C-N-P) during the sedimentation process, contributing to the Earth's C-N-P balance. However, the mechanisms underlying C-N-P stoichiometry in response to intensive human activity and organic matter sources remain underexplored, especially in freshwater ecosystems. This study identifies the temporal patterns of C-N-P stoichiometry, reveals the inner driving factors, and clarifies its impact path, especially in eutrophication (the late 1970s). The results revealed that sediment RCP and RNP increased significantly and were controlled by TCAR and TNAR, respectively, indicating the direct impact of burial rate on C-N-P stoichiometry. Based on redundancy analysis and the STM model, autochthonous origin, GDP, and population had positive effects on sediment TCAR, TNAR, and TPAR, which, in turn, affected RCN, RCP, and RNP. Organic matter sources and human activities have a significant influence on RCN, RCP, and RNP, possibly regulated by the variation of TCAR and TNAR. Autochthonous origin had an indirect positive impact on RCN and RCP through the mediating effect of TCAR. Similarly, through the mediating effect of TNAR, it had an indirect negative impact on RCN and an indirect positive impact on RNP. This study showed that TCAR, TNAR, TPAR, GDP, autochthonous, allochthonous and population better explained the changes in RCN, RCP, and RNP over a-hundred-year deposition, highlighting an in-depth understanding of the dynamic change mechanism of sediment C-N-P stoichiometry during the lake deposition process.

Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth

Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.

Microbial communities drive flux of acid orange 7 and crystal violet dyes in water-sediment system

Unchecked dye effluent discharge poses escalating environmental and economic concerns, especially in developing nations. While dyes are well-recognized water pollutants, the mechanisms of their environmental spread are least understood. Therefore, the present study examines the partitioning of Acid Orange 7 (AO7) and Crystal Violet (CV) dyes using water-sediment microcosms and reports that native microbes significantly affect AO7 decolorization and transfer. Both dyes transition from infused to pristine matrices, reaching equilibrium in a fortnight. While microbes influence CV partitioning, their role in decolorization is minimal, emphasizing their varied impact on the environmental fate of dyes. Metagenomic analyses reveal contrasting microbial composition between control and AO7-infused samples. Control water samples displayed a dominance of Proteobacteria (62%), Firmicutes (24%), and Bacteroidetes (9%). However, AO7 exposure led to Proteobacteria reducing to 57% and Bacteroidetes to 3%, with Firmicutes increasing to 34%. Sediment samples, primarily comprising Firmicutes (47%) and Proteobacteria (39%), shifted post-AO7 exposure: Proteobacteria increased to 53%, and Firmicutes dropped to 38%. At the genus level, water samples dominated by Niveispirillum (34%) declined after AO7 exposure, while Bacillus and Pseudomonas increased. Notably, Serratia and Sphingomonas, known for azo dye degradation, rose post-exposure, hinting at their role in AO7 decolorization. Conversely, sediment samples showed a decrease in the growth of Bacillus and an increase in that of Pseudomonas and Serratia. These findings emphasize the significant role of microbial communities in determining the environmental fate of dyes, providing insights on its environmental implications and management.

Structural insights of a SusD-like protein in marine Bacteroidetes bacteria reveal the molecular basis for chitin recognition and acquisition

Efficient recognition and transportation of chitin oligosaccharides are crucial steps for the utilization of chitin by heterotrophic bacteria. In this study, we employed structural biological and biochemical approaches to investigate the substrate recognition and acquisition mechanism of a novel chitin-binding SusD-like protein, AqSusD, which is derived from the chitin utilization gene cluster of a marine Bacteroides strain (Aquimarina sp. SCSIO 21287). We resolved the crystal structures of the AqSusD apo-protein and its complex with chitin oligosaccharides. Our results revealed that some crucial residues (Gln67, Phe87, and Asp276) underwent significant conformational changes to form tighter substrate binding sites for ligand binding. Moreover, we identified the functions of key amino acid residues and discovered that π-π stacking and hydrogen bonding between AqSusD and the ligand played significant roles in recognition of the protein for chitin oligosaccharide binding. Based on our findings and previous investigations, we put forward a model for the mechanism of chitin oligosaccharide recognition, capture, and transport by AqSusD, in collaboration with the membrane protein AqSusC. Our study deepens the understanding of the molecular-level "selfish" use of polysaccharides such as chitin by Bacteroides.

Collaborative metabolisms of urea and cyanate degradation in marine anammox bacterial culture

Anammox process greatly contributes to nitrogen loss occurring in oceanic oxygen minimum zones (OMZs), where the availability of NH4+ is scarce as compared with NO2-. Remineralization of organic nitrogen compounds including urea and cyanate (OCN-) into NH4+ has been believed as an NH4+ source of the anammox process in oxygen minimum zones. However, urea- or OCN-- dependent anammox has not been well examined due to the lack of marine anammox bacterial culture. In the present study, urea and OCN- degradation in a marine anammox bacterial consortium were investigated based on 15N-tracer experiments and metagenomic analysis. Although a marine anammox bacterium, Candidatus Scalindua sp., itself was incapable of urea and OCN- degradation, urea was anoxically decomposed to NH4+ by the coexisting ureolytic bacteria (Rhizobiaceae, Nitrosomonadaceae, and/or Thalassopiraceae bacteria), whereas OCN- was abiotically degraded to NH4+. The produced NH4+ was subsequently utilized in the anammox process. The activity of the urea degradation increased under microaerobic condition (ca. 32-42 μM dissolved O2, DO), and the contribution of the anammox process to the total nitrogen loss also increased up to 33.3% at 32 μM DO. Urea-dependent anammox activities were further examined in a fluid thioglycolate media with a vertical gradient of O2 concentration, and the active collaborative metabolism of the urea degradation and anammox was detected at the lower oxycline (21 μM DO).

Environmental gradients shape microbiome assembly and stability in the East China sea

Microbiomes play a key role in marine ecosystem functioning and sustainability. Their organization and stability in coastal areas, particularly in anthropogenic-influenced regions, however, remains unclear compared with an understanding of how microbial community shifts respond to marine environmental gradients. Here, the assembly and community associations across vertical and horizontal gradients in the East China Sea are systematically researched. The seawater microbial communities possessed higher robustness and lower fragmentation and vulnerability compared to the sediment microbiomes. Spatial gradients act as a deterministic filtering factor for microbiome organization. Microbial communities had lower phylogenetic distance and higher niche breadth in the nearshore and offshore areas compared to intermediate areas. The phylogenetic distance of microbiomes decreased from the surface to the bottom but the niche breadth was enhanced in surface and bottom environments. Vertical gradients destabilized microbial associations, while the community diversity was enhanced. Multivariate regression tree analysis and canonical correspondence analysis indicated that depth, distance from shore, nutrient availability, temperature, salinity, and chlorophyll a, affected the distribution and co-occurrence of microbial groups. Our results highlight the crucial roles of environmental gradients in determining microbiome association and stability. These results improve our understanding of the survival strategies/adaptive mechanisms of microbial communities in response to environmental variation and provide new insights for protecting the ecosystems and maintaining the sustainability of ecological functions.

New insights on the role of nitrogen in the resistance to environmental stress in an endosymbiotic dinoflagellate

Endosymbiotic dinoflagellates provide the nutritional basis for marine invertebrates, especially reef-building corals. These dinoflagellates are sensitive to environmental changes, and understanding the factors that can increase the resistance of the symbionts is crucial for the elucidation of the mechanisms involved with coral bleaching. Here, we demonstrate how the endosymbiotic dinoflagellate Durusdinium glynnii is affected by concentration (1760 vs 440 µM) and source (sodium nitrate vs urea) of nitrogen after light and thermal stress exposure. The effectiveness in the use of the two nitrogen forms was proven by the nitrogen isotopic signature. Overall, high nitrogen concentrations, regardless of source, increased D. glynnii growth, chlorophyll-a, and peridinin levels. During the pre-stress period, the use of urea accelerated the growth of D. glynnii compared to cells grown using sodium nitrate. During the luminous stress, high nitrate conditions increased cell growth, but no changes in pigments composition was observed. On the other hand, during thermal stress, a steep and steady decline in cell densities over time was observed, except for high urea condition, where there is cellular division and peridinin accumulation 72 h after the thermal shock. Our findings suggest peridinin has a protective role during the thermal stress, and the uptake of urea by D. glynnii can alleviate thermal stress responses, eventually mitigating coral bleaching events.

The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms

The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.

Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone

Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales. It is unclear whether such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions, distinguishing free-living microbes versus particle-associated microbes. We find a substantial increase in the nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in the modulation of the C:N ratios of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes that are involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers. IMPORTANCE The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability being known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example, along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to the interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses by using metagenomes from the nitracline of the eastern tropical North Pacific OMZ, including both particle-associated and nonassociated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micrometer to millimeter scale associated with particle-associated versus free-living lifestyles.

Optimizing heterotrophic production of Chlorella sorokiniana SU-9 proteins potentially used as a sustainable protein substitute in aquafeed

Alternative protein sources for the reduction/replacement of fish meal in aqua-feeds are in urgent demand. Microalgae are considered sustainable protein sources for aquaculture due to their high-quality proteins with a complete profile of essential amino acids. This study examined the heterotrophic production of proteins from Chlorella sorokiniana SU-9. Culture parameters for maximal biomass and protein production are as follows: glucose - 10 g/L glucose, sodium nitrate - 1.5 g/L, and iron - 46 μM iron in BG-11 medium. Under optimal conditions, biomass content, protein content and protein productivity of SU-9 reached 4.14 ± 0.20 g/L, 403 ± 33 mg/g and 382 ± 36 mg/L/d, respectively. The protein profile of Chlorella sorokiniana SU-9 is comparable to fishmeal and soybean meal. The essential amino acids arginine, lysine and cysteine, along with glutamine and glutamate, were high. The production cost of SU-9 can be significantly reduced under heterotrophic cultivation conditions, making it a potential protein substitute in aquafeed.

Genomic analysis of Marinimicrobium sp. C6131 reveals its genetic potential involved in chitin metabolism

Marinimicrobium sp. C6131, which had the ability to degrade chitin, was isolated from deep-sea sediment of the southwest Indian Ocean. Here, the genome of strain C6131 was sequenced and the chitin metabolic pathways were constructed. The genome contained a circular chromosome of 4,207,651 bp with a G + C content of 58.50%. A total of 3471 protein-coding sequences were predicted. Gene annotation and metabolic pathway reconstruction showed that strain C6131 possessed genes and two metabolic pathways involved in chitin catabolism: the hydrolytic chitin utilization pathway initiated by chitinases and the oxidative chitin utilization pathway initiated by lytic polysaccharide monooxygenases. Chitin is the most abundant polysaccharide in the ocean. Degradation and recycling of chitin driven by marine bacteria are crucial for biogeochemical cycles of carbon and nitrogen in the ocean. The genomic information of strain C6131 revealed its genetic potential involved in chitin metabolism. The strain C6131 could grow with colloidal chitin as the sole carbon source, indicating that these genes would have functions in chitin degradation and utilization. The genomic sequence of Marinimicrobium sp. C6131 could provide fundamental information for future studies on chitin degradation, and help to improve our understanding of the chitin degradation process in deep-sea environments.

Regulatory and metabolic adaptations in the nitrogen assimilation of marine picocyanobacteria

Prochlorococcus and Synechococcus are the two most abundant photosynthetic organisms on Earth, with a strong influence on the biogeochemical carbon and nitrogen cycles. Early reports demonstrated the streamlining of regulatory mechanisms in nitrogen metabolism and the removal of genes not strictly essential. The availability of a large series of genomes, and the utilization of latest generation molecular techniques have allowed elucidating the main mechanisms developed by marine picocyanobacteria to adapt to the environments where they thrive, with a particular interest in the strains inhabiting oligotrophic oceans. Given that nitrogen is often limited in those environments, a series of studies have explored the strategies utilized by Prochlorococcus and Synechococcus to exploit the low concentrations of nitrogen-containing molecules available in large areas of the oceans. These strategies include the reduction in the GC and the cellular protein contents; the utilization of truncated proteins; a reduced average amount of N in the proteome; the development of metabolic mechanisms to perceive and utilize nanomolar nitrate concentrations; and the reduced responsiveness of key molecular regulatory systems such as NtcA to 2-oxoglutarate. These findings are in sharp contrast with the large body of knowledge obtained in freshwater cyanobacteria. We will outline the main discoveries, stressing their relevance to the ecological success of these important microorganisms.

The Saccharina latissima microbiome: Effects of region, season, and physiology

Introduction

Saccharina latissima is a canopy-forming species of brown algae and, as such, is considered an ecosystem engineer. Several populations of this alga are exploited worldwide, and a decrease in the abundance of S. latissima at its southern distributional range limits has been observed. Despite its economic and ecological interest, only a few data are available on the composition of microbiota associated with S. latissima and its role in algal physiologyn.

Methods

We studied the whole bacterial community composition associated with S. latissima samples from three locations (Brittany, Helgoland, and Skagerrak) by 16S metabarcoding analyses at different scales: algal blade part, regions, season (at one site), and algal physiologic state.

Results and Discussion

We have shown that the difference in bacterial composition is driven by factors of decreasing importance: (i) the algal tissues (apex/meristem), (ii) the geographical area, (iii) the seasons (at the Roscoff site), and (iv) the algal host's condition (healthy vs. symptoms). Overall, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia dominated the general bacterial communities. Almost all individuals hosted bacteria of the genus Granulosicoccus, accounting for 12% of the total sequences, and eight additional core genera were identified. Our results also highlight a microbial signature characteristic for algae in poor health independent of the disease symptoms. Thus, our study provides a comprehensive overview of the S. latissima microbiome, forming a basis for understanding holobiont functioning.

The Co-Evolution Aspects of the Biogeochemical Role of Phytoplankton in Aquatic Ecosystems: A Review

In freshwater and marine ecosystems, the phytoplankton community is based on microalgae and cyanobacteria, which include phylogenetically very diverse groups of oxygenic photoautotrophs. In the process of evolution, they developed a wide range of bio(geo)chemical adaptations that allow them to effectively use solar radiation, CO₂, and nutrients, as well as major and trace elements, to form O₂ and organic compounds with a high chemical bond energy. The inclusion of chemical elements in the key processes of energy and plastic metabolism in the cell is determined by redox conditions and the abundance and metabolic availability of elements in the paleoenvironment. Geochemical evolution, which proceeded simultaneously with the evolution of biosystems, contributed to an increase in the number of metals and trace elements acting as cofactors of enzymes involved in metabolism and maintaining homeostasis in the first photoautotrophs. The diversity of metal-containing enzymes and the adaptive ability to replace one element with another without losing the functional properties of enzymes ensured the high ecological plasticity of species and allowed microalgae and cyanobacteria to successfully colonize a wide variety of habitats. In this review, we consider the main aspects of the modern concepts of the biogeochemical evolution of aquatic ecosystems and the role of some metals in the main bioenergetic processes in photosynthetic prokaryotes and eukaryotes. We present generalized data on the efficiency of the assimilation of key nutrients by phytoplankton and their importance in the cycle of carbon, silicon, nitrogen, phosphorus, sulfur, and iron. This article presents modern views on the evolutionary prerequisites for the formation of elemental signatures in different systematic groups of microalgae, as well as the possibility of using the stoichiometric ratio in the study of biological and geochemical processes in aquatic ecosystems.

Nitrous oxide emission in altered nitrogen cycle and implications for climate change

Natural processes and human activities play a crucial role in changing the nitrogen cycle and increasing nitrous oxide (N₂O) emissions, which are accelerating at an unprecedented rate. N₂O has serious global warming potential (GWP), about 310 times higher than that of carbon dioxide. The food production, transportation, and energy required to sustain a world population of seven billion have required dramatic increases in the consumption of synthetic nitrogen (N) fertilizers and fossil fuels, leading to increased N₂O in air and water. These changes have radically disturbed the nitrogen cycle and reactive nitrogen species, such as nitrous oxide (N₂O), and have impacted the climatic system. Yet, systematic and comprehensive studies on various underlying processes and parameters in the altered nitrogen cycle, and their implications for the climatic system are still lacking. This paper reviews how the nitrogen cycle has been disturbed and altered by anthropogenic activities, with a central focus on potential pathways of N₂O generation. The authors also estimate the N₂O-N emission mainly due to anthropogenic activities will be around 8.316 Tg N₂O-N yr^-1 in 2050. In order to minimize and tackle the N₂O emissions and its consequences on the global ecosystem and climate change, holistic mitigation strategies and diverse adaptations, policy reforms, and public awareness are suggested as vital considerations. This study concludes that rapidly increasing anthropogenic perturbations, the identification of new microbial communities, and their role in mediating biogeochemical processes now shape the modern nitrogen cycle.

A pathway for chitin oxidation in marine bacteria

Oxidative degradation of chitin, initiated by lytic polysaccharide monooxygenases (LPMOs), contributes to microbial bioconversion of crystalline chitin, the second most abundant biopolymer in nature. However, our knowledge of oxidative chitin utilization pathways, beyond LPMOs, is very limited. Here, we describe a complete pathway for oxidative chitin degradation and its regulation in a marine bacterium, Pseudoalteromonas prydzensis. The pathway starts with LPMO-mediated extracellular breakdown of chitin into C1-oxidized chitooligosaccharides, which carry a terminal 2-(acetylamino)-2-deoxy-D-gluconic acid (GlcNAc1A). Transmembrane transport of oxidized chitooligosaccharides is followed by their hydrolysis in the periplasm, releasing GlcNAc1A, which is catabolized in the cytoplasm. This pathway differs from the known hydrolytic chitin utilization pathway in enzymes, transporters and regulators. In particular, GlcNAc1A is converted to 2-keto-3-deoxygluconate 6-phosphate, acetate and NH₃ via a series of reactions resembling the degradation of D-amino acids rather than other monosaccharides. Furthermore, genomic and metagenomic analyses suggest that the chitin oxidative utilization pathway may be prevalent in marine Gammaproteobacteria.

Low-Ammonium Environment Increases the Nutrient Exchange between Diatom-Diazotroph Association Cells and Facilitates Photosynthesis and N2 Fixation-a Mechanistic Modeling Analysis

Diatom–diazotroph associations (DDAs) are one of the most important symbiotic dinitrogen (N₂) fixing groups in the oligotrophic ocean. Despite their capability to fix N₂, ammonium (NH₄⁺) remains a key nitrogen (N) source for DDAs, and the effect of NH₄⁺ on their metabolism remains elusive. Here, we developed a coarse-grained, cellular model of the DDA with NH₄⁺ uptake and quantified how the level of extracellular NH₄⁺ influences metabolism and nutrient exchange within the symbiosis. The model shows that, under a fixed growth rate, an increased NH₄⁺ concentration may lower the required level of N₂ fixation and photosynthesis, and decrease carbon (C) and N exchange. A low-NH₄⁺ environment leads to more C and N in nutrient exchange and more fixed N₂ to support a higher growth rate. With higher growth rates, nutrient exchange and metabolism increased. Our study shows a strong effect of NH₄⁺ on metabolic processes within DDAs, and thus highlights the importance of in situ measurement of NH₄⁺ concentrations.

Performance and mechanism of tetracycline removal by the aerobic nitrate-reducing strain Pseudomonas sp. XS-18 with auto-aggregation

The coexistence of multiple pollutants has become a distinctive feature of water pollution. However, there are a few strains that can remove nitrate and tetracycline (TC). Here, the efficiency of strain XS-18 in removing nitrate and TC was analyzed, and the mechanism of tolerance and removal of TC was investigated by infrared spectroscopy, three-dimensional fluorescence spectroscopy, and genome analysis. XS-18 could efficiently remove TC (0.40 mg·L^-1·h^-1) at pH 7.0-11.0 with auto-aggregation. TC was removed via extracellular polymeric substance (EPS) (55.90%) and cell surface (44.10%) adsorption. TC (10 mg/L) could stimulate XS-18 to secrete more polysaccharides and hydrophobic proteins to improve its auto-aggregation ability. The findings also confirmed that TC resistance genes were present. Furthermore, the bacterial flagellum, signal transduction of the chemotactic system and regulatory genes were shown to be related to the auto-aggregation of the strain. XS-18 has potential applications in the treatment of wastewater containing nitrate and TC.

Kelp carbon sink potential decreases with warming due to accelerating decomposition

Cycling of organic carbon in the ocean has the potential to mitigate or exacerbate global climate change, but major questions remain about the environmental controls on organic carbon flux in the coastal zone. Here, we used a field experiment distributed across 28° of latitude, and the entire range of 2 dominant kelp species in the northern hemisphere, to measure decomposition rates of kelp detritus on the seafloor in relation to local environmental factors. Detritus decomposition in both species were strongly related to ocean temperature and initial carbon content, with higher rates of biomass loss at lower latitudes with warmer temperatures. Our experiment showed slow overall decomposition and turnover of kelp detritus and modeling of coastal residence times at our study sites revealed that a significant portion of this production can remain intact long enough to reach deep marine sinks. The results suggest that decomposition of these kelp species could accelerate with ocean warming and that low-latitude kelp forests could experience the greatest increase in remineralization with a 9% to 42% reduced potential for transport to long-term ocean sinks under short-term (RCP4.5) and long-term (RCP8.5) warming scenarios. However, slow decomposition at high latitudes, where kelp abundance is predicted to expand, indicates potential for increasing kelp-carbon sinks in cooler (northern) regions. Our findings reveal an important latitudinal gradient in coastal ecosystem function that provides an improved capacity to predict the implications of ocean warming on carbon cycling. Broad-scale patterns in organic carbon decomposition revealed here can be used to identify hotspots of carbon sequestration potential and resolve relationships between carbon cycling processes and ocean climate at a global scale.

Estimations of 137Cs activity concentrations using marine parameters issued from MODIS and Copernicus Marine Environment Monitoring Services (CMEMS) data in Souda Bay (Crete, Greece) for the period 2011-2019

Cesium-137, as the main fission product, is of special interest in the marine environment because of its solubility, which results to very low sinking time. Nevertheless, the conservative form of the main percentage of ¹³⁷Cs introduced in the marine environment (70%) makes ¹³⁷Cs to be included in the salinity of sea water. Based on this property, in this study, we examine potential relations between ¹³⁷Cs activity concentrations and marine parameters issued from Earth Observation (EO) data products in the Southern Aegean Sea, in order to investigate the possibility of ¹³⁷Cs to be recorded by satellite data. In particular, measurements of physical and biological marine parameters issued from the Copernicus Marine Environment Monitoring Service (CMEMS) database and MODIS ocean products are retrieved for the dates of ¹³⁷Cs field measurements. Single and multiple regression analyses are performed between the marine parameters and ¹³⁷Cs activity concentration measurements for three distinctive time periods (total, cold, and warm period). The best results are obtained from multiple regressions, one for each time period (r² > 0.70). The models show that during cold period, ¹³⁷Cs activity concentrations are highly correlated to both chlorophyll and nutrients (phosphates) while during warm and the total period, they seem to be mainly correlated to the photosynthetic available incident solar radiation on the sea surface. For each period, we propose a multiparameter model linear in its parameters. Although the results of this study must be considered preliminary due to the limited size of the datasets, for the first time, we show that estimations of ¹³⁷Cs activity concentrations from EO measurements and CMEMS environmental models are feasible, and they can be used as a marine radiological assessment tool for a closed Mediterranean bay such as Souda Bay in Greece.

Dark Diazotrophy during the Late Summer in Surface Waters of Chile Bay, West Antarctic Peninsula

Although crucial for the addition of new nitrogen in marine ecosystems, dinitrogen (N2) fixation remains an understudied process, especially under dark conditions and in polar coastal areas, such as the West Antarctic Peninsula (WAP). New measurements of light and dark N2 fixation rates in parallel with carbon (C) fixation rates, as well as analysis of the genetic marker nifH for diazotrophic organisms, were conducted during the late summer in the coastal waters of Chile Bay, South Shetland Islands, WAP. During six late summers (February 2013 to 2019), Chile Bay was characterized by high NO3− concentrations (~20 µM) and an NH4+ content that remained stable near 0.5 µM. The N:P ratio was approximately 14.1, thus close to that of the Redfield ratio (16:1). The presence of Cluster I and Cluster III nifH gene sequences closely related to Alpha-, Delta- and, to a lesser extent, Gammaproteobacteria, suggests that chemosynthetic and heterotrophic bacteria are primarily responsible for N2 fixation in the bay. Photosynthetic carbon assimilation ranged from 51.18 to 1471 nmol C L−1 d−1, while dark chemosynthesis ranged from 9.24 to 805 nmol C L−1 d−1. N2 fixation rates were higher under dark conditions (up to 45.40 nmol N L−1 d−1) than under light conditions (up to 7.70 nmol N L−1 d−1), possibly contributing more than 37% to new nitrogen-based production (≥2.5 g N m−2 y−1). Of all the environmental factors measured, only PO43- exhibited a significant correlation with C and N2 rates, being negatively correlated (p < 0.05) with dark chemosynthesis and N2 fixation under the light condition, revealing the importance of the N:P ratio for these processes in Chile Bay. This significant contribution of N2 fixation expands the ubiquity and biological potential of these marine chemosynthetic diazotrophs. As such, this process should be considered along with the entire N cycle when further reviewing highly productive Antarctic coastal waters and the diazotrophic potential of the global marine ecosystem.

A Comprehensive Network Integrating Signature Microbes and Crucial Soil Properties During Early Biological Soil Crust Formation on Tropical Reef Islands

Biological soil crusts (BSCs/biocrusts), which are distributed across various climatic zones and well-studied in terrestrial drylands, harbor polyextremotolerant microbial topsoil communities and provide ecological service for local and global ecosystem. Here, we evaluated BSCs in the tropical reef islands of the South China Sea. Specifically, we collected 41 BSCs, subsurface, and bare soil samples from the Xisha and Nansha Archipelagos. High-throughput amplicon sequencing was performed to analyze the bacterial, fungal, and archaeal compositions of these samples. Physicochemical measurement and enzyme activity assays were conducted to characterize the soil properties. Advanced computational analysis revealed 47 biocrust-specific microbes and 10 biocrust-specific soil properties, as well as their correlations in BSC microbial community. We highlighted the previously underestimated impact of manganese on fungal community regulation and BSC formation. We provide comprehensive insight into BSC formation networks on tropical reef islands and established a foundation for BSC-directed environmental restoration.

Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean

Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on “who is doing what, where, and how?”, this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory—determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly.

Nitrate Water Contamination from Industrial Activities and Complete Denitrification as a Remediation Option

Freshwater is a scarce resource that continues to be at high risk of pollution from anthropogenic activities, requiring remediation in such cases for its continuous use. The agricultural and mining industries extensively use water and nitrogen (N)-dependent products, mainly in fertilizers and explosives, respectively, with their excess accumulating in different water bodies. Although removal of NO3 from water and soil through the application of chemical, physical, and biological methods has been studied globally, these methods seldom yield N2 gas as a desired byproduct for nitrogen cycling. These methods predominantly cause secondary contamination with deposits of chemical waste such as slurry brine, nitrite (NO2), ammonia (NH3), and nitrous oxide (N2O), which are also harmful and fastidious to remove. This review focuses on complete denitrification facilitated by bacteria as a remedial option aimed at producing nitrogen gas as a terminal byproduct. Synergistic interaction of different nitrogen metabolisms from different bacteria is highlighted, with detailed attention to the optimization of their enzymatic activities. A biotechnological approach to mitigating industrial NO3 contamination using indigenous bacteria from wastewater is proposed, holding the prospect of optimizing to the point of complete denitrification. The approach was reviewed and found to be durable, sustainable, cost effective, and environmentally friendly, as opposed to current chemical and physical water remediation technologies.

The sRNA NsiR4 fine-tunes arginine synthesis in the cyanobacterium Synechocystis sp. PCC 6803 by post-transcriptional regulation of PirA

As the only oxygenic phototrophs among prokaryotes, cyanobacteria employ intricate mechanisms to regulate common metabolic pathways. These mechanisms include small protein inhibitors exerting their function by protein-protein interaction with key metabolic enzymes and regulatory small RNAs (sRNAs). Here we show that the sRNA NsiR4, which is highly expressed under nitrogen limiting conditions, interacts with the mRNA of the recently described small protein PirA in the model strain Synechocystis sp. PCC 6803. In particular, NsiR4 targets the pirA 5'UTR close to the ribosome binding site. Heterologous reporter assays confirmed that this interaction interferes with pirA translation. PirA negatively impacts arginine synthesis under ammonium excess by competing with the central carbon/nitrogen regulator P_II that binds to and thereby activates the key enzyme of arginine synthesis, N-acetyl-L-glutamate-kinase (NAGK). Consistently, ectopic nsiR4 expression in Synechocystis resulted in lowered PirA accumulation in response to ammonium upshifts, which also affected intracellular arginine pools. As NsiR4 and PirA are inversely regulated by the global nitrogen transcriptional regulator NtcA, this regulatory axis enables fine tuning of arginine synthesis and conveys additional metabolic flexibility under highly fluctuating nitrogen regimes. Pairs of small protein inhibitors and of sRNAs that control the abundance of these enzyme effectors at the post-transcriptional level appear as fundamental building blocks in the regulation of primary metabolism in cyanobacteria.

Comparative analysis of microbial communities between water and sediment in Laoshan Bay marine ranching with varied aquaculture activities

We profiled and compared the bacterial and protist community compositions and dynamics in the Laoshan Bay marine ranching involving varied aquaculture activities. The dominant species, differential species and community compositions among the five aquaculture areas, two habitats and two periods were significantly different. The relationships between microbial communities and environmental factors were analyzed. We found that microbial communities in the water were more sensitive to the environmental changes than sediment, and the responses of bacterial and protist communities to the disturbances were varied. To meet the challenges of higher aquaculture density, the proportion of the positive correlations among co-occurrence networks in the water increased markedly from July to November; while the positive proportion in the sediment was stable. Potential ecological interactions and keystone taxa between bacteria and protists were studied. These results advanced our understanding of how mariculture stressors affect microbial communities in marine ranching.

Distribution of Dissolved Nitrogen Compounds in the Water Column of a Meromictic Subarctic Lake

In order to better understand the biogeochemical cycle of nitrogen in meromictic lakes, which can serve as a model for past aquatic environments, we measured dissolved concentrations of nitrate, nitrite, ammonium, and organic nitrogen in the deep (39 m maximal depth) subarctic Lake Svetloe (NW Russia). The lake is a rare type of freshwater meromictic water body with high concentrations of methane, ferrous iron, and manganese and low concentrations of sulfates and sulfides in the monimolimnion. In the oligotrophic mixolimnion, the concentration of mineral forms of nitrogen decreased in summer compared to winter, likely due to a phytoplankton bloom. The decomposition of the bulk of the organic matter occurs under microaerophilic/anaerobic conditions of the chemocline and is accompanied by the accumulation of nitrogen in the form of N-NH4 in the monimolimnion. We revealed a strong relationship between methane and nitrogen cycles in the chemocline and monimolimnion horizons. The nitrate concentrations in Lake Svetloe varied from 9 to 13 μM throughout the water column. This fact is rare for meromictic lakes, where nitrate concentrations up to 13 µM are found in the monimolimnion zone down to the bottom layers. We hypothesize, in accord with available data for other stratified lakes that under conditions of high concentrations of manganese and ammonium at the boundary of redox conditions and below, anaerobic nitrification with the formation of nitrate occurs. Overall, most of the organic matter in Lake Svetloe undergoes biodegradation essentially under microaerophilic/anaerobic conditions of the chemocline and the monimolimnion. Consequently, the manifestation of the biogeochemical nitrogen cycle is expressed in these horizons in the most vivid and complex relationship with other cycles of elements.

Alterations to sediment nutrient deposition and transport along a six reservoir sequence

Reservoir presence and construction has become commonplace along rivers due to the multitude of ecosystem services they provide. Many services are well recognized, including the effectiveness of sequestering both sediments and sediment-bound nutrients such as silts and phosphorus (P). Reservoirs are also capable of transforming or sequestering significant quantities of nutrients with more complex biogeochemical pathways, like nitrogen (N). Reservoir assessments, independent of inflow-outflow models, have primarily focused on a small number of systems creating a growing need to understand how reservoirs function both individually and as reservoir sequences within large rivers and their watersheds. Models have simulated the overall efficiency and drivers of reservoir nutrient deposition, but few have considered how a sequence of reservoirs alters deposition as an interdependent watershed-sediment-transport-system. In this study, we collected sediment cores from a six-reservoir sequence along a 5th - 6th order stream receiving treated waters from a large metropolitan area in the subtropical southeastern United States. Paleolimnological studies of subtropical reservoirs are underrepresented and are needed to understand the history of reservoir development. Using paleolimnological techniques and a known 30 year flux of riverine nutrient loading from waste water treatment facilities, we compared nutrient deposition to reservoir morphological qualities and primary producer community structure during the past ~50 years. Our findings suggest phosphorus deposition is associated with reservoir order downstream of the primary nutrient source, nitrogen deposition is linked to reservoir water retention time, and N:P is most strongly linked to reservoir surface area and watershed population density. Our results were strongly influenced by a large upstream and metropolitan nutrient source, common in large rivers, but under different conditions of nutrient loading (i.e. nonpoint source), reservoirs may express other nutrient depositional patterns.

Tracking Microbial Evolution in the Subseafloor Biosphere

The deep marine subsurface constitutes a massive biosphere that hosts a multitude of archaea, bacteria, and viruses across a diversity of habitats. These microbes play key roles in mediating global biogeochemical cycles, and the marine subsurface is thought to have been among the earliest habitats for life on Earth. Yet we have a poor understanding of what forces govern the evolution of subsurface microbes over time. Here, I outline why evolutionary trajectories in the subsurface may be different than those of microbes living on the surface of the planet and describe how we can take advantage of technological advancements to study the evolutionary dynamics of subsurface microbes and their viruses. The sequencing revolution, in tandem with marine infrastructure advancements, promises that we will soon gain a much deeper understanding of how the vast majority of the microbial biosphere changes, adapts, and evolves over time.

Structures and function of the amino acid polymerase cyanophycin synthetase

Cyanophycin is a natural biopolymer produced by a wide range of bacteria, consisting of a chain of poly-L-Asp residues with L-Arg residues attached to the β-carboxylate sidechains by isopeptide bonds. Cyanophycin is synthesized from ATP, aspartic acid and arginine by a homooligomeric enzyme called cyanophycin synthetase (CphA1). CphA1 has domains that are homologous to glutathione synthetases and muramyl ligases, but no other structural information has been available. Here, we present cryo-electron microscopy and X-ray crystallography structures of cyanophycin synthetases from three different bacteria, including cocomplex structures of CphA1 with ATP and cyanophycin polymer analogs at 2.6 Å resolution. These structures reveal two distinct tetrameric architectures, show the configuration of active sites and polymer-binding regions, indicate dynamic conformational changes and afford insight into catalytic mechanism. Accompanying biochemical interrogation of substrate binding sites, catalytic centers and oligomerization interfaces combine with the structures to provide a holistic understanding of cyanophycin biosynthesis.

Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments

In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of an AOA (AOA-AC1) and an AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp. and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. Is79, belonged to the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM and AOB-G5-7 at 500 μM. These findings indicate that, during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Importance Nitrification is an important process in the global nitrogen cycle. The first step - ammonia oxidation to nitrite - can be carried out by Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.

In situ SERS detection of dissolved nitrate on hydrated gold substrates

The accurate and fast measurement of nitrate in seawater is important for monitoring and controlling water quality to prevent ecologic and economic disasters. In this work we show that the in situ detection of nitrate in aqueous solution is feasible at nanomolar concentrations through surface enhanced Raman spectroscopy (SERS) using native nanostructured gold substrates without surface functionalization. Spectra were analyzed as collected or after standard normal variate (SNV) normalization, which was shown through Principal Component Analysis (PCA) to reduce spectral variations between sample sets and improve Langmuir adsorption model fits. An additional normalization approach based on the substrate silicon template showed that silicon provided an internal standard that accounted for the spectral variance without the need for SNV normalization. Nitrate adsorption was well-described by the Langmuir adsorption model, consistent with an adsorbed monolayer, and a limit of detection of 64 nM nitrate was obtained in ultrapure water, representing environmentally relevant concentrations. Free energy calculations based on the Langmuir adsorption constants, approximating equilibrium adsorption constants, and calculated self-energy arising from image charge, accounting for electrostatic interactions with a polarizable nanostructured substrate, suggest that nitrate adsorption was partially driven by an entropy gain presumably due to dehydration of the gold substrate and/or nitrate ion. This work is being extended to determine if similar statistical and normalization methods can be applied to nitrate detection in complex natural waters where non-target ions and molecules are expected to interfere.

Reclamation-induced tidal restriction increases dissolved carbon and greenhouse gases diffusive fluxes in salt marsh creeks

Intertidal creeks play an important role in transporting nutrients between coastal ecosystems and ocean. Reclamation is a predominant anthropogenic disturbance in coastal regions; however, the influence of reclamation on carbon and nitrogen species and greenhouse gas (GHG) fluxes in creek remains unclear. In a subtropical salt marsh of eastern China, the seasonal patterns of dissolved carbon (DOC, DIC, CO₂, and CH₄) and inorganic nitrogen (NH₄⁺-N, NO₂^--N, and NO₃^--N and N₂O) species, and the diffusive fluxes of CO₂, CH₄, and N₂O, were compared between the natural tidal creeks and the reclaimed creeks. Due to notably changed hydrological and biological conditions in the reclaimed creeks, concentrations of all dissolved carbon species, NH₄⁺-N and NO₂^--N increased significantly by 60.2-288.2%, while NO₃^--N and N₂O decreased slightly, compared to the natural tidal creeks. DIC and NO₃^--N were the primary components of the total dissolved carbon and inorganic nitrogen in both creek types; however, their proportions decreased as a result of elevated DOC, CO₂, CH₄, NH₄⁺-N, and NO₂^--N following reclamation. Significantly higher global warming potential (0.58 ± 0.15 g CO₂-eq m^-2 d^-1) was found in the reclaimed creeks, making them hotspot of greenhouse effects, compared to the natural tidal creeks. Our results indicated that changes in flow velocity, salinity, Chlorophyll a, and pH were the main factors controlling the dissolved carbon and nitrogen and consequent GHG emissions, due to reclamation. This study is helpful in understanding of carbon and nitrogen sink-source shifts resulting from land use changes in coastal wetlands.

Microbiome Analysis Reveals Microecological Balance in the Emerging Rice-Crayfish Integrated Breeding Mode

The interaction between the microbial communities in aquatic animals and those in the ambient environment is important for both healthy aquatic animals and the ecological balance of aquatic environment. Crayfish (Procambarus clarkii), with their high commercial value, have become the highest-yield freshwater shrimp in China. The traditional cultivation in ponds (i.e., monoculture, MC) and emerging cultivation in rice co-culture fields (i.e., rice–crayfish co-culture, RC) are the two main breeding modes for crayfish, and the integrated RC is considered to be a successful rice-livestock integration practice in eco-agricultural systems. This study explored the ecological interactions between the microbial communities in crayfish intestine and the ambient environment, which have not been fully described to date. The bacterial communities in crayfish intestine, the surrounding water, and sediment in the two main crayfish breeding modes were analyzed with MiSeq sequencing and genetic networks. In total, 53 phyla and 1,206 genera were identified, among which Proteobacteria, Actinobacteria, Tenericutes, Firmicutes, Cyanobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, RsaHF231, and Nitrospirae were the dominant phyla. The microbiota composition significantly differed between the water, sediment, and crayfish intestine, while it did not between the two breeding modes. We also generated a co-occurrence correlation network based on the high-confidence interactions with Spearman correlation ρ ≥ 0.75. In the genera co-correlation network, 95 nodes and 1,158 edges were identified, indicating significant genera interactions between crayfish intestine and the environment. Furthermore, the genera clustered into three modules, based on the different environments. Additionally, Candidatus_Bacilloplasma, g_norank_f_Steroidobacteraceae, Dinghuibacter, Hydrogenophaga, Methyloparacoccus, and Defluviicoccus had the highest betweenness centrality and might be important in the interaction between crayfish and the ambient environment. Overall, this study enhances our understanding of the characteristics of the microbiota in crayfish and their surrounding environment. Moreover, our findings provide insights into the microecological balance in crayfish eco-agricultural systems and theoretical reference for the development of such systems.

Salt-Tolerant Metabolomics for Exometabolomic Measurements of Marine Bacterial Isolates

Identifying and quantifying metabolites secreted by microbial isolates can aid in understanding the physiological traits of diverse species and their interaction with the environment. Mass spectrometry-based metabolomics has potential to provide a holistic view of the exometabolism of marine isolates, but the high salt content of such samples interferes with chromatography and ionization during the measurement of polar exometabolites. The most common desalting methods are faced with major limitations, including limited separation of small polar metabolites from salts, the use of organic solvents that cannot accommodate large salt quantities, and sample throughput. Here, we utilize a cyano stationary phase to develop a high-throughput, isocratic liquid chromatography-mass spectrometry (LC-MS) desalting method that mitigates these shortcomings. We demonstrate that counterions present in a common marine growth medium experience distinct elution times, which prevents their coelution with 73 physiologically relevant polar metabolites, effectively minimizing the effects of salt content on ion suppression. We determined optimal salt concentrations for quadrupole time-of-flight (QTOF) MS measurements and limits of quantification in the low micromolar range in the salty matrix. The efficacy of this method was demonstrated through the measurement of exometabolites secreted by three marine bacterial isolates originating from a carrageenan degrading microbial community. This method provides a simple, versatile desalting method for measuring exometabolites of environmental isolates and other biological matrices.

Quantifying potential N turnover rates in hypersaline microbial mats by 15N tracer techniques

Microbial mats, due to stratification of the redox zones, have a potential to include a complete N cycle, however an attempt to evaluate a complete N cycle in these ecosystems has not been yet made. In this study, occurrence and rates of major N cycle processes were evaluated in intact microbial mats from Elkhorn Slough, Monterey Bay, CA, USA, and Baja California Sur, Mexico under oxic and anoxic conditions using ¹⁵N-labeling techniques. All of the major N transformation pathways, with the exception of anammox, were detected in both microbial mats. Nitrification rates were found to be low at both sites for both seasons investigated. The highest rates of ammonium assimilation were measured in Elkhorn Slough mats in April and corresponded to high in situ ammonium concentration in the overlying water. Baja mats featured higher ammonification than ammonium assimilation rates and this, along with their higher affinity for nitrate compared to ammonium and low dissimilatory nitrate reduction to ammonium rates, characterized their differences from Elkhorn Slough mats. Nitrogen fixation rates in Elkhorn Slough microbial mats were found to be low implying that other processes such as recycling and assimilation from water are main sources of N for these mats at the times sampled. Denitrification in all of the mats was incomplete with nitrous oxide as end product and not dinitrogen. Our findings highlight N cycling features not previously quantified in microbial mats and indicate a need of further investigations in these microbial ecosystems.Importance: Nitrogen is essential for life. The nitrogen cycle on Earth is mediated by microbial activity and has had a profound impact on both the atmosphere and the biosphere throughout geologic time. Microbial mats, present in many modern environments, have been regarded as living records of the organisms, genes, and phylogenies of microbes, as they are one of the most ancient ecosystems on Earth. While rates of major nitrogen metabolic pathways have been evaluated in a number of ecosystems, it remains elusive in microbial mats. In particular it is unclear what factors affect nitrogen cycling in these ecosystems and how morphological differences between mats impact nitrogen transformations. In this study we investigate nitrogen cycling in two microbial mats having morphological differences. Our findings provide insight for further understanding of biogeochemistry and microbial ecology of microbial mats.

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific

Nitrification is a vital ecosystem function in the open ocean that regenerates inorganic nitrogen and promotes primary production. Recent studies have shown that the ecology and physiology of nitrifying organisms is more complex than previously postulated. The distribution of these organisms in the remote oligotrophic ocean and their interactions with the physicochemical environment are relatively understudied. In this work, we aimed to evaluate the depth profile of nitrifying archaea and bacteria in the Eastern North Pacific Subtropical Front, an area with limited biological surveys but with intense trophic transferences and physicochemical gradients. Furthermore, we investigated the dominant physicochemical and biological relationships within and between ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) as well as with the overall prokaryotic community. We used a 16S rRNA gene sequencing approach to identify and characterize the nitrifying groups within the first 500 m of the water column and to analyze their abiotic and biotic interactions. The water column was characterized mainly by two contrasting environments, warm O₂-rich surface waters with low dissolved inorganic nitrogen (DIN) and a cold O₂-deficient mesopelagic layer with high concentrations of nitrate (NO₃^–). Thaumarcheotal AOA and bacterial NOB were highly abundant below the deep chlorophyll maximum (DCM) and in the mesopelagic. In the mesopelagic, AOA and NOB represented up to 25 and 3% of the total prokaryotic community, respectively. Interestingly, the AOA community in the mesopelagic was dominated by unclassified genera that may constitute a novel group of AOA highly adapted to the conditions observed at those depths. Several of these unclassified amplicon sequence variants (ASVs) were positively correlated with NO₃^– concentrations and negatively correlated with temperature and O₂, whereas known thaumarcheotal genera exhibited the opposite behavior. Additionally, we found a large network of positive interactions within and between putative nitrifying ASVs and other prokaryotic groups, including 13230 significant correlations and 23 sub-communities of AOA, AOB, NOB, irrespective of their taxonomic classification. This study provides new insights into our understanding of the roles that AOA may play in recycling inorganic nitrogen in the oligotrophic ocean, with potential consequences to primary production in these remote ecosystems.

Metagenomic Analysis Reveals Microbial Community Structure and Metabolic Potential for Nitrogen Acquisition in the Oligotrophic Surface Water of the Indian Ocean

Despite being the world’s third largest ocean, the Indian Ocean is one of the least studied and understood with respect to microbial diversity as well as biogeochemical and ecological functions. In this study, we investigated the microbial community and its metabolic potential for nitrogen (N) acquisition in the oligotrophic surface waters of the Indian Ocean using a metagenomic approach. Proteobacteria and Cyanobacteria dominated the microbial community with an average 37.85 and 23.56% of relative abundance, respectively, followed by Bacteroidetes (3.73%), Actinobacteria (1.69%), Firmicutes (0.76%), Verrucomicrobia (0.36%), and Planctomycetes (0.31%). Overall, only 24.3% of functional genes were common among all sampling stations indicating a high level of gene diversity. However, the presence of 82.6% common KEGG Orthology (KOs) in all samples showed high functional redundancy across the Indian Ocean. Temperature, phosphate, silicate and pH were important environmental factors regulating the microbial distribution in the Indian Ocean. The cyanobacterial genus Prochlorococcus was abundant with an average 17.4% of relative abundance in the surface waters, and while 54 Prochlorococcus genomes were detected, 53 were grouped mainly within HLII clade. In total, 179 of 234 Prochlorococcus sequences extracted from the global ocean dataset were clustered into HL clades and exhibited less divergence, but 55 sequences of LL clades presented more divergence exhibiting different branch length. The genes encoding enzymes related to ammonia metabolism, such as urease, glutamate dehydrogenase, ammonia transporter, and nitrilase presented higher abundances than the genes involved in inorganic N assimilation in both microbial community and metagenomic Prochlorococcus population. Furthermore, genes associated with dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification and anammox were absent in metagenome Prochlorococcus population, i.e., nitrogenase and nitrate reductase. Notably, the de novo biosynthesis pathways of six different amino acids were incomplete in the metagenomic Prochlorococcus population and Prochlorococcus genomes, suggesting compensatory uptake of these amino acids from the environment. These results reveal the features of the taxonomic and functional structure of the Indian Ocean microbiome and their adaptive strategies to ambient N deficiency in the oligotrophic ocean.

N2O and NOy production by the comammox bacterium Nitrospira inopinata in comparison with canonical ammonia oxidizers

Nitrous oxide (N₂O) and NO_y (nitrous acid (HONO) + nitric oxide (NO) + nitrogen dioxide (NO₂)) are released as byproducts or obligate intermediates during aerobic ammonia oxidation, and further influence global warming and atmospheric chemistry. The ammonia oxidation process is catalyzed by groups of globally distributed ammonia-oxidizing microorganisms, which are playing a major role in atmospheric N₂O and NO_y emissions_. Yet, little is known about HONO and NO₂ production by the recently discovered, widely distributed complete ammonia oxidizers (comammox), able to individually perform the oxidation of ammonia to nitrate via nitrite. Here, we examined the N₂O and NO_y production patterns by comammox bacterium Nitrospira inopinata during aerobic ammonia oxidation, in comparison to its canonical ammonia-converting counterparts, representatives of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings, i) show low yield NO_y production by the comammox bacterium compared to AOB; ii) highlight the role of the NO reductase in the biological formation of N₂O based on results from NH₂OH inhibition assays and its stimulation during archaeal and bacterial ammonia oxidations; iii) postulate that the lack of hydroxylamine (NH₂OH) and NO transformation enzymatic activities may lead to a buildup of NH₂OH/NO which can abiotically react to N₂O ; iv) collectively confirm restrained N₂O and NO_y emission by comammox bacteria, an unneglectable consortium of microbes in global atmospheric emission of reactive nitrogen gases.

Novel microbial nitrogen transformation processes in constructed wetlands treating municipal sewage: a mini-review

Traditionally nitrogen transformation in constructed wetlands (CWs) has been attributed to the activities of aerobic autotrophic nitrifiers followed by anoxic heterotrophic denitrifiers. However, the nitrogen balances in such systems are far from being explained as a large fraction of the losses remain unaccounted for. The classical nitrification-denitrification theory has been successfully employed in certain unit processes by culturing fast-growing bacteria, but the CWs offer an ideal environment for slow-growing bacteria that may be beneficially exploited to achieve enhanced nitrogen removal by manipulating the environmental conditions in their favor. In the last three decades, many novel microorganisms have been isolated from CWs that have led to the discovery of some other routes that have made researchers believe could play a significant role in nitrogen transformation processes. The increased understanding of novel discerned pathways like anaerobic ammonium oxidation (ANAMMOX), heterotrophic nitrification and aerobic denitrification, which are mediated by specialized bacteria has indicated that these microorganisms could be enriched by applying selection pressures within CWs for achieving high rates of nitrogen removal. Understanding these novel nitrogen transformation processes along with the associated microbial population can provide new dimensions to the design of CWs for enhanced nitrogen removal.

Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands

Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.

Reduction of alternative electron acceptors drives biofilm formation in Shewanella algae

Shewanella spp. possess a broad respiratory versatility, which contributes to the occupation of hypoxic and anoxic environmental or host-associated niches. Here, we observe a strain-specific induction of biofilm formation in response to supplementation with the anaerobic electron acceptors dimethyl sulfoxide (DMSO) and nitrate in a panel of Shewanella algae isolates. The respiration-driven biofilm response is not observed in DMSO and nitrate reductase deletion mutants of the type strain S. algae CECT 5071, and can be restored upon complementation with the corresponding reductase operon(s) but not by an operon containing a catalytically inactive nitrate reductase. The distinct transcriptional changes, proportional to the effect of these compounds on biofilm formation, include cyclic di-GMP (c-di-GMP) turnover genes. In support, ectopic expression of the c-di-GMP phosphodiesterase YhjH of Salmonella Typhimurium but not its catalytically inactive variant decreased biofilm formation. The respiration-dependent biofilm response of S. algae may permit differential colonization of environmental or host niches.

Seasonal modulation of phytoplankton biomass in the Southern Ocean

Over the last ten years, satellite and geographically constrained in situ observations largely focused on the northern hemisphere have suggested that annual phytoplankton biomass cycles cannot be fully understood from environmental properties controlling phytoplankton division rates (e.g., nutrients and light), as they omit the role of ecological and environmental loss processes (e.g., grazing, viruses, sinking). Here, we use multi-year observations from a very large array of robotic drifting floats in the Southern Ocean to determine key factors governing phytoplankton biomass dynamics over the annual cycle. Our analysis reveals seasonal phytoplankton accumulation ('blooming') events occurring during periods of declining modeled division rates, an observation that highlights the importance of loss processes in dictating the evolution of the seasonal cycle in biomass. In the open Southern Ocean, the spring bloom magnitude is found to be greatest in areas with high dissolved iron concentrations, consistent with iron being a well-established primary limiting nutrient in this region. Under ice observations show that biomass starts increasing in early winter, well before sea ice begins to retreat. The average theoretical sensitivity of the Southern Ocean to potential changes in seasonal nutrient and light availability suggests that a 10% change in phytoplankton division rate may be associated with a 50% reduction in mean bloom magnitude and annual primary productivity, assuming simple changes in the seasonal magnitude of phytoplankton division rates. Overall, our results highlight the importance of quantifying and accounting for both division and loss processes when modeling future changes in phytoplankton biomass cycles.

Unusual marine cyanobacteria/haptophyte symbiosis relies on N2 fixation even in N-rich environments

The microbial fixation of N₂ is the largest source of biologically available nitrogen (N) to the oceans. However, it is the most energetically expensive N-acquisition process and is believed inhibited when less energetically expensive forms, like dissolved inorganic N (DIN), are available. Curiously, the cosmopolitan N₂-fixing UCYN-A/haptophyte symbiosis grows in DIN-replete waters, but the sensitivity of their N₂ fixation to DIN is unknown. We used stable isotope incubations, catalyzed reporter deposition fluorescence in-situ hybridization (CARD-FISH), and nanoscale secondary ion mass spectrometry (nanoSIMS), to investigate the N source used by the haptophyte host and sensitivity of UCYN-A N₂ fixation in DIN-replete waters. We demonstrate that under our experimental conditions, the haptophyte hosts of two UCYN-A sublineages do not assimilate nitrate (NO₃⁻) and meet little of their N demands via ammonium (NH₄⁺) uptake. Instead the UCYN-A/haptophyte symbiosis relies on UCYN-A N₂ fixation to supply large portions of the haptophyte’s N requirements, even under DIN-replete conditions. Furthermore, UCYN-A N₂ fixation rates, and haptophyte host carbon fixation rates, were at times stimulated by NO₃⁻ additions in N-limited waters suggesting a link between the activities of the bulk phytoplankton assemblage and the UCYN-A/haptophyte symbiosis. The results suggest N₂ fixation may be an evolutionarily viable strategy for diazotroph–eukaryote symbioses, even in N-rich coastal or high latitude waters.

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms.

Video Abstract

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A catalog of 47 million genes was generated from 370 globally distributed metagenomes

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Meta-omics data integration disentangled the mechanisms of changes in transcript pools

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Transcript pool changes of metabolic marker genes show distinct mechanistic patterns

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Community turnover as a response to ocean warming may be strongest in polar regions

Abundance, diversity, and distribution patterns along with the salinity of four nitrogen transformation-related microbes in the Yangtze Estuary

Purpose

The abundance and composition of nitrogen transformation-related microbes with certain environmental parameters for living conditions provide information about the nitrogen cycle in the Yangtze Estuary. The aim of this study was to explore the impacts of salinity on four N-related microbes and reveal the phylogenetic characteristics of microorganisms in the Yangtze Estuary ecosystem. A molecular biology method was used for the quantitation and identification of four microbes in the Yangtze River: ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying microbes (nirS-type), and anaerobic ammonia-oxidizing (anammox) bacteria. Sequence identification was performed on the levels of phylum, class, order, family, and genus, and the sequences were then matched to species.

Result

The results showed that the dominant species of AOA were crenarchaeote enrichment cultures, thaumarchaeote enrichment cultures, and Nitrosopumilus maritimus cultures, and the dominant AOB species were betaproteobacterium enrichment cultures and Nitrosomona sp. The denitrifying microbes were identified as the phylum Proteobacteria, classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, and the species Thauera selenatis. The dominant species of the anammox bacteria was Candidatus Brocadia sp. In the estuarine sediments of the Yangtze River, the nirS gene abundance (1.31 × 107–9.50 × 108 copies g−1 sediments) was the highest among all the detected genes, and the abundance of bacterial amoA, archaeal amoA, and nirS was significantly correlated. Closely correlated with the abundance of the bacterial amoA gene, salinity was an important factor in promoting the abundance and restraining the community diversity of AOB. Moreover, the distribution of the AOB species exhibited regional patterns in the estuarine zone.

Conclusions

The results indicated that salinity might promote abundance while limiting the diversity of AOB and that salinity might have reverse impacts on AOA. Denitrifying microbes, which showed a significant correlation with the other genes, were thought to interact with the other genes during nitrogen migration. The results also implied that AOA has a lower potential nitrification rate than AOB and that both the anammox and denitrification processes (defined by nirS gene) account for N2 production.

Limited evidence for common interannual trends in Baltic Sea summer phytoplankton biomass

The Baltic Sea summer phytoplankton community plays an important role in biogeochemical cycling and in the transfer of energy through the food web via zooplankton. We aimed to improve the understanding of the degree to which large-scale versus local environmental dynamics regulate phytoplankton dynamics by analyzing time series at the Baltic Sea scale. We used dynamic factor analysis to study if there are common patterns of interannual variation that are shared (“common trends”) among summer phytoplankton total and class-level biomass time series observed across Baltic Sea latitudinal gradients in salinity and temperature. We evaluated alternative hypotheses regarding common trends among summer phytoplankton biomass: Baltic Sea-wide common trends; common trends by geography (latitude and basin); common trends differing among functional groups (phytoplankton classes); or common trends driven by both geography and functional group. Our results indicated little support for a common trend in total summer phytoplankton biomass. At a finer resolution, classes had common trends that were most closely associated with the cryptophyte and cyanobacteria time series with patterns that differed between northern and southern sampling stations. These common trends were also very sensitive to two anomalous years (1990, 2008) of cryptophyte biomass. The Baltic Sea Index, a regional climate index, was correlated with two common class trends that shifted in mean state around the mid-1990s. The limited coherence in phytoplankton biomass variation over time despite known, large-scale, ecosystem shifts suggests that stochastic dynamics at local scales limits the ability to observe common trends at the scale of monitoring data collection.