Global Nutrient Cycles Research Articles

Exploring river nitrogen and phosphorus loading and export to global coastal waters in the Shared Socio-economic pathways

This global spatially explicit (0.5 by 0.5 degree) analysis presents the nitrogen (N) and phosphorus (P) inputs, processing and biogeochemical retention and delivery to surface waters and river export to coastal seas according to the five shared socioeconomic pathways (SSP). Four systems are considered: (i) human system; (ii) agriculture; (iii) aquaculture; (iv) nature. Exploring the changes during 1980–2015 and 2015–2050 according to the SSPs shows that the natural nutrient sources have been declining in the past decades and will continue to decline in all SSPs in future decades due to massive land transformations, while agriculture, human sewage and aquaculture are becoming increasingly dominant (globally up to 80% of nutrient delivery). More efforts than those employed in any of the SSPs are needed to slow down the global nutrient cycles. One of the drivers of the proliferation of harmful algal blooms is the tendency towards increasing N:P ratios in global freshwaters and export to the global coastal seas; this is the result of increasing N:P in inputs in food production, more efficient biogeochemical retention of P than of N in river basins, and groundwater N legacies, which seems to be most pronounced in a united world that strives after sustainability. The diverging strategies to achieve UN Sustainable Development Goals 14 (life below water), 2 (zero hunger) and 6 (clean water and sanitation) therefore require a balanced management system for both N and P in all systems, that accounts for future nutrient legacies.

Tradeoffs and Synergies in Tropical Forest Root Traits and Dynamics for Nutrient and Water Acquisition: Field and Modeling Advances

Vegetation processes are fundamentally limited by nutrient and water availability, the uptake of which is mediated by plant roots in terrestrial ecosystems. While tropical forests play a central role in global water, carbon, and nutrient cycling, we know very little about tradeoffs and synergies in root traits that respond to resource scarcity. Tropical trees face a unique set of resource limitations, with rock-derived nutrients and moisture seasonality governing many ecosystem functions, and nutrient versus water availability often separated spatially and temporally. Root traits that characterize biomass, depth distributions, production and phenology, morphology, physiology, chemistry, and symbiotic relationships can be predictive of plants’ capacities to access and acquire nutrients and water, with links to aboveground processes like transpiration, wood productivity, and leaf phenology. In this review, we identify an emerging trend in the literature that tropical fine root biomass and production in surface soils are greatest in infertile or sufficiently moist soils. We also identify interesting paradoxes in tropical forest root responses to changing resources that merit further exploration. For example, specific root length, which typically increases under resource scarcity to expand the volume of soil explored, instead can increase with greater base cation availability, both across natural tropical forest gradients and in fertilization experiments. Also, nutrient additions, rather than reducing mycorrhizal colonization of fine roots as might be expected, increased colonization rates under scenarios of water scarcity in some forests. Efforts to include fine root traits and functions in vegetation models have grown more sophisticated over time, yet there is a disconnect between the emphasis in models characterizing nutrient and water uptake rates and carbon costs versus the emphasis in field experiments on measuring root biomass, production, and morphology in response to changes in resource availability. Closer integration of field and modeling efforts could connect mechanistic investigation of fine-root dynamics to ecosystem-scale understanding of nutrient and water cycling, allowing us to better predict tropical forest-climate feedbacks.

Protistan-Bacterial Microbiota Exhibit Stronger Species Sorting and Greater Network Connectivity Offshore than Nearshore across a Coast-to-Basin Continuum

ABSTRACTLittle is known regarding how community assembly and species association vary with habitat and depth. Here, we examined the assembly and association of protistan and bacterial communities across a coast-shelf-slope-basin gradient of the South China Sea using high-throughput sequencing of the V3 and V4 regions of the rRNA gene transcript. Our study revealed that homogenizing dispersal and drift exerted an influence on protistan communities comparable to that on bacterial communities. In contrast, selection and dispersal limitation exerted contrasting effects on the two microbial communities. Community assembly was governed to a greater degree by selection than by dispersal limitation in the bacterial community, and this was much lower in the protistan community. Moreover, this organismal assembly pattern was robust with habitat and depth. However, the relative importance of selection to dispersal limitation varied with habitat and depth in both communities, where horizontally it was higher offshore than nearshore and vertically it was lower in the bottom or deep chlorophyll maximum (DCM) than on the surface. The offshore possessed more microbial network complexity and more associations among microbial taxa than the nearshore, and vertically, the bottom possessed more complexity than the surface and the DCM. Moreover, temperature is strongly associated with the composition and co-occurrence of microbial communities, implying that temperature plays a dominant role in the selection of the protistan-bacterial microbiome across a coast-to-basin continuum. This study contributes to our understanding of the assembly mechanism and species association of protistan-bacterial microbiota across multiple habitats and depths.IMPORTANCE Microbial organisms play a crucial role in global nutrient cycling. Few studies have attempted to simultaneously investigate the community assembly of microeukaryotes and prokaryotes and their association patterns in oceanic waters. This is especially true regarding how they vary with habitats and depths despite the fact that they are essential for developing a more holistic understanding of marine ecosystems. This study revealed the differential actions of selection and dispersal limitation and species association across a coast-to-basin continuum on the marine protistan-bacterial microbiome. Moreover, temperature was identified as a crucial factor driving the structure and co-occurrence of protistan and bacterial communities. The results emphasize that the differences in community assembly and association patterns between nearshore and offshore of the main constituents of the ocean microbiota should be considered to understand their current and future configurations. This is especially crucial in the context of climate change, as the response of ocean microbiota to nearshore and offshore temperature changes remains unknown.

Mycorrhizal Distributions Impact Global Patterns of Carbon and Nutrient Cycling

AbstractMost tree species predominantly associate with a single type of mycorrhizal fungi, which can differentially affect plant nutrient acquisition and biogeochemical cycling. Uncertainties in mycorrhizal distributions are non‐trivial, and current estimates disagree in up to 50% over 40% of the land area, including tropical forests. Remote sensing capabilities for mycorrhizal detection show promise for refining these estimates further. Here, we address for the first time the impact of mycorrhizal distributions on global carbon and nutrient cycling. Using the state‐of‐the‐art carbon‐nitrogen economics within the Community Land Model version 5, we found Net Primary Productivity (NPP) increased throughout the 21st century by 20%; however, as soil nitrogen has progressively become limiting, the costs to NPP for nitrogen acquisition—that is, to mycorrhizae—have increased at a faster rate by 60%. This suggests that nutrient acquisition will increasingly demand a higher portion of assimilated carbon to support the same productivity.

Benthic exchange along a tropical estuarine salinity gradient during dry season: Biogeochemical and ecological implications

Benthic biogeochemistry and its coupling with pelagic ecology are less understood in tropical than in temperate estuaries, which have significant implications for global carbon and nutrient cycling. In dry season, the Mandovi Estuary of Western India develops a prominent salinity gradient (0–35 psu), and remains nutrient-limited but most productive, which stands in contrast to wet season. To understand the role of benthic exchange in the sustenance of estuarine biogeochemistry and ecosystem, we carried out biogeochemical measurements in the water column and a series of intact-core incubations along the estuarine salinity gradient, during the dry season of 2014. We observed that the lower estuary was nitrogen (N)-limited whereas the middle and upper estuary were phosphorus (P)-limited. The benthic respiration (38.6–82.87 mmol O2 m−2 d−1), organic carbon (Corg) mineralization (34.3–79.8 mmol C m−2 d−1) and nutrient exchange rates considerably varied along the salinity gradient. Variability in benthic respiration was apparently controlled by labile Corg content and faunal abundance in the sediments. Benthic exchange of NH4+ and NOx− were mainly controlled by salinity and NOx− of the water column, respectively. Benthic PO43− exchange was predominantly controlled by sedimentary Fe content and bottom water O2, whereas benthic SiO44− exchange was primarily controlled by sediment-water SiO44− gradient. Abiotic processes accounted for 37-79% of sediment O2 consumption (SOC). Benthic metabolism accounted for 34–60% of total community respiration and mineralized 43–145% equivalent of C fixed through primary production (PP). Of dissolved inorganic nitrogen (DIN) efflux (0.67–2.59 mmol m−2 d−1), NH4+ comprised 91% in the lower estuary but NOx− (NO3− + NO2−) comprised 97% in the upper estuary, and benthic nitrification apparently determined the dominant N species released from the sediments. Coupled nitrification-denitrification apparently caused the loss of 30–69% of NH4+ diffusing from the deeper sediments. The estuarine sediments were a net source of DIN and SiO44−, potentially meeting up to 31% of N and 40% of Si demand of the phytoplankton, but acted as a net PO43− sink owing to high sedimentary Fe and normoxia, and tended to buffer the estuarine water PO43− to 0.05–0.19 μM. Benthic PO43− influx (0.006–0.026 mmol m−2 d−1) apparently caused the P-limiting condition in the middle and upper estuary. Particularly, the role benthic DIN supply was crucial for the sustenance of estuarine PP as the estuary receives some PO43− from the sea and sufficient SiO44− from the river but not sufficient DIN. The sediments potentially immobilized up to 25% and 20% of riverine DIN and PO43− load, respectively. Overall, the study revealed an efficient benthic carbon recycling and a tight benthic-pelagic coupling in the estuary during the dry season.

The Ecology and Evolution of Model Microbial Mutualisms

Mutually beneficial interspecific interactions are abundant throughout the natural world, including between microbes. Mutualisms between microbes are critical for everything from human health to global nutrient cycling. Studying model microbial mutualisms in the laboratory enables highly controlled experiments for developing and testing evolutionary and ecological hypotheses. In this review, we begin by describing the tools available for studying model microbial mutualisms. We then outline recent insights that laboratory systems have shed on the evolutionary origins, evolutionary dynamics, and ecological features of microbial mutualism. We touch on gaps in our current understanding of microbial mutualisms, note connections to mutualism in nonmicrobial systems, and call attention to open questions ripe for future study.

Southern Ocean Oxygenation Changes Inferred From Redox‐Sensitive Trace Metals Across Marine Isotope Stage 11

AbstractChanges in the circulation of the Southern Ocean are known to have impacted global nutrient, heat, and carbon cycles during the glacial and interglacial periods of the late Pleistocene. Proxy‐based records of these changes deserve continued scrutiny as the implications may be important for constraining future change. A record of authigenic uranium from the South Atlantic has been used to infer changes in deep‐sea oxygenation and organic matter export over the past 0.5 million years. Since sedimentary uranium has the possible complication of remobilization, it is prudent to investigate the behavior of other redox‐sensitive trace metals to confidently interpret temporal changes in oxygenation. Focusing here on the exceptionally long interglacial warm period, Marine Isotope Stage (MIS) 11, we found concurrent authigenic enrichments of uranium (U) and rhenium (Re) throughout MIS 12 to 10, overall supporting prior interpretations of low‐oxygen periods. However, there are differential responses of Re and U to oxygen changes and some evidence of small‐scale Re remobilization, which may involve differences in molecular‐level reduction mechanisms. Peaks in authigenic manganese (Mn) intervening with peaks in Re and U indicate increases in porewater oxygenation which likely relate to increased Antarctic Bottom Water circulation at the onset of MIS11c and during the peak warmth of the interglacial around 400 ka.

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups.

Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa.

Sequence-Specific Capture of Oligonucleotide Probes (SCOPE): a Simple and Rapid Microbial rRNA Quantification Method Using a Molecular Weight Cutoff Membrane.

A method named sequence-specific capture of oligonucleotide probes (SCOPE) was developed for quantification of microbial rRNA molecules in a multiplex manner. In this method, a molecular weight cutoff membrane (MWCOM) was used for the separation of fluorescence-labeled oligonucleotide probes hybridized with rRNA from free unhybridized probes. To demonstrate proof of concept, probes targeting bacteria or archaea at different taxonomic levels were prepared and were hybridized with rRNAs. The hybridization stringency was controlled by adjusting reaction temperature and urea concentration in the mixture. Then, the mixture was filtered through the MWCOM. The rRNA and hybridized probes collected on the MWCOM were recovered and quantified using a spectrophotometer and fluorospectrometer, respectively. The method showed high accuracy in detecting specific microbial rRNA in a defined nucleic acid mixture. Furthermore, the method was capable of simultaneous detection and quantification of multiple target rRNAs in a sample with sensitivity up to a single-base mismatch. The SCOPE method was tested and benchmarked against reverse transcription-quantitative PCR (RT-qPCR) for the quantification of Bacteria, Archaea, and some key methanogens in anaerobic sludge samples. It was observed that the SCOPE method produced more reliable and coherent results. Thus, the SCOPE method allows simple and rapid detection and quantification of target microbial rRNAs for environmental microbial population analysis without any need for enzymatic reactions. IMPORTANCE Microorganisms play integral roles in the Earth's ecosystem. Microbial populations and their activities significantly affect the global nutrient cycles. Quantification of key microorganisms provides important information that is required to understand their roles in the environment. Sequence-based analysis of microbial population is a powerful tool, but it provides information only on relative abundance of microorganisms. Hence, the development of a simpler and quick method for the quantification of microorganisms is necessary. To address the shortcomings of a variety of molecular methods reported so far, we developed a simple, rapid, accurate, and multiplexed microbial rRNA quantification method to evaluate the abundance of specific microbial populations in complex ecosystems. This method demonstrated high specificity, reproducibility, and applicability to such samples. The method is useful for quantitative detection of particular microbial members in the environment.

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt.

Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.

A novel ATP dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA.

Dimethylsulfoniopropionate (DMSP) is an abundant and ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling. Diverse DMSP lyases in some algae, bacteria, and fungi cleave DMSP to yield gaseous dimethyl sulfide (DMS), an infochemical with important roles in atmospheric chemistry. Here, we identified a novel ATP-dependent DMSP lyase, DddX. DddX belongs to the acyl-CoA synthetase superfamily and is distinct from the eight other known DMSP lyases. DddX catalyses the conversion of DMSP to DMS via a two-step reaction: the ligation of DMSP with CoA to form the intermediate DMSP-CoA, which is then cleaved to DMS and acryloyl-CoA. The novel catalytic mechanism was elucidated by structural and biochemical analyses. DddX is found in several Alphaproteobacteria, Gammaproteobacteria, and Firmicutes, suggesting that this new DMSP lyase may play an overlooked role in DMSP/DMS cycles.

Brassica napus phyllosphere bacterial composition changes with growth stage

AimsPhyllosphere bacteria play critical roles in plant growth promotion, disease suppression and global nutrient cycling but remain understudied.MethodsIn this project, we examined the bacterial community on the phyllosphere of eight diverse lines of Brassica napus for ten weeks in Saskatoon, Saskatchewan Canada.ResultsThe bacterial community was shaped largely by plant growth stage with distinct communities present before and after flowering. Bacterial diversity before flowering had 111 core members with high functional potential, with the peak of diversity being reached during flowering. After flowering, bacterial diversity dropped quickly and sharply to 16 members of the core community, suggesting that the plant did not support the same functional potential anymore. B. napus line had little effect on the larger community, but appeared to have more of an effect on the rare bacteria.ConclusionsOur work suggests that the dominant bacterial community is driven by plant growth stage, whereas differences in plant line seemed to affect rare bacteria. The role of these rare bacteria in plant health remains unresolved.

Influence of settling organic matter quantity and quality on benthic nitrogen cycling

AbstractCoastal sediments are major contributors to global carbon (C) mineralization and nutrient cycling and are tightly linked to processes in the pelagic environment. In this study, we aimed to investigate the regulating potential of quantity and quality of planktonic organic matter (OM) deposition on benthic metabolism, with a particular focus on nitrogen (N) cycling processes. We simulated inputs of spring (C : N 10.9) and summer (C : N 5.6) plankton communities in high and low quantities to sediment cores, and followed oxygen consumption, nutrient fluxes as well as nitrate reduction rates, that is, denitrification and dissimilatory nitrate reduction to ammonium for 10 d. Our results demonstrate the primary importance of OM quality in determining the fate of organic N once it settles to the sediment surface. Settling of N‐rich summer plankton material resulted in a ∼ twofold lower denitrification efficiency (40–56%) compared to N‐poor spring plankton (88–115%). This indicates that N‐rich plankton deposition favors recycling of inorganic nutrients to the water column over N‐loss via denitrification. OM quantity was positively related to mineralization activity, but this neither directly affected N fluxes nor denitrification activity, highlighting the complex interplay between the OM quantity and quality in regulating N cycling. In light of these new findings, we support the use of simple qualitative indicators such as C : N ratio of OM to investigate how future changes in benthic‐pelagic coupling might influence N budgets at the sediment–water interface.

Microbial community shifts reflect losses of native soil carbon with pyrogenic and fresh organic matter additions and are greatest in low-carbon soils.

Soil organic carbon (SOC) plays an important role in regulating global climate change, carbon and nutrient cycling in soils, and soil moisture. Organic matter (OM) additions to soils can affect the rate at which SOC is mineralized by microbes, with potentially important effects on SOC stocks. Understanding how pyrogenic organic matter (PyOM) affects the cycling of native SOC (nSOC) and the soil microbes responsible for these effects is important for fire-affected ecosystems as well as for biochar-amended systems. We used an incubation trial with five different soils from National Ecological Observatory Network sites across the US and 13C-labelled 350°C corn stover PyOM and fresh corn stover OM to trace nSOC-derived CO2 emissions with and without PyOM and OM amendments. We used high-throughput sequencing of rRNA genes to characterize bacterial, archaeal, and fungal communities and their response to PyOM and OM in soils that were previously stored at -80°C. We found that the effects of amendments on nSOC-derived CO2 reflected the unamended soil C status, where relative increases in C mineralization were greatest in low-C soils. OM additions produced much greater effects on nSOC-CO2 emissions than PyOM additions. Furthermore, the magnitude of microbial community composition change mirrored the magnitude of increases in nSOC-CO2, indicating a specific subset of microbes were likely responsible for the observed changes in nSOC mineralization. However, PyOM responders differed across soils and did not necessarily reflect a common "charosphere". Overall, this study suggests that soils that already have low SOC may be particularly vulnerable to short-term increases in SOC loss with OM or PyOM additions.Importance Soil organic matter (SOM) has an important role in global climate change, carbon and nutrient cycling in soils, and soil moisture dynamics. Understanding the processes that affect SOM stocks is important for managing these functions. Recently, understanding how fire-affected organic matter (or "pyrogenic" organic matter (PyOM)) affects existing SOM stocks has become increasingly important, both due to changing fire regimes, and to interest in "biochar" - pyrogenic organic matter that is produced intentionally for carbon management or as an agricultural soil amendment. We found that soils with less SOM were more prone to increased losses with PyOM (and fresh organic matter) additions, and that soil microbial communities changed more in soils that also had greater SOM losses with PyOM additions. This suggests that soils that already have low SOM content may be particularly vulnerable to short-term increases in SOM loss, and that a subset of the soil microbial community is likely responsible for these effects.

An observation-based evaluation and ranking of historical Earth system model simulations in the northwest North Atlantic Ocean

Abstract. Continental shelf regions in the ocean play an important role in the global cycling of carbon and nutrients, but their responses to global change are understudied. Global Earth system models (ESMs), as essential tools for building understanding of ocean biogeochemistry, are used extensively and routinely for projections of future climate states; however, their relatively coarse spatial resolution is likely not appropriate for accurately representing the complex patterns of circulation and elemental fluxes on the shelves along ocean margins. Here, we compared 29 ESMs used in the Intergovernmental Panel on Climate Change (IPCC)'s Assessment Reports (ARs) 5 and 6 and a regional biogeochemical model for the northwest North Atlantic (NWA) shelf to assess their ability to reproduce surface observations of temperature, salinity, nitrate and chlorophyll. The NWA region is biologically productive, influenced by the large-scale Gulf Stream and Labrador Current systems and particularly sensitive to climatically induced changes in large-scale circulation. Most ESMs compare relatively poorly to observed surface nitrate and chlorophyll and show differences with observed surface temperature and salinity that suggest spatial mismatches in their large-scale current systems. Model-simulated nitrate and chlorophyll compare better with available observations in AR6 than in AR5, but none of the models perform equally well for all four parameters. The ensemble means of all ESMs, and of the five best-performing ESMs, strongly underestimate observed chlorophyll and nitrate. The regional model has a much higher spatial resolution and reproduces the observations significantly better than any of the ESMs. It also simulates reasonably well vertically resolved observations from gliders and bi-monthly ship-based monitoring observations. A ranking of the ESMs indicates that only one ESM has good and consistent performance for all variables. An additional evaluation of the ESMs along the regional model boundaries shows larger variability but is generally consistent with the ranking on the shelf. Overall, 11 ESMs were deemed satisfactory for use in the NWA, either directly or for regional downscaling.

Global patterns in leaf stoichiometry across coastal wetlands

AbstractAimCoastal wetlands provide crucial ecosystem functions and services, such as coastal protection, nutrient retention and C sequestration. Despite the important roles in global C, N and P cycling, the global variation in leaf stoichiometry across coastal wetlands remains unclear.LocationGlobal.Time period1980–2018.Major taxa studiedVascular plants.MethodsBy compiling a global dataset of 698 data records in 205 sites, we carried out systematic analyses of the world‐wide trends and their determinants of leaf element contents and ratios of plants across coastal wetlands.ResultsLeaf N and P contents increased significantly, but C:N, C:P and N:P ratios decreased with increasing latitude in coastal wetlands. The mean annual temperature was the predominant driver of leaf N, P and C:N, whereas soil N:P was a good predictor of leaf C:P and N:P ratios. Furthermore, N increased faster with P in plant leaves of coastal wetlands compared with terrestrial ecosystems. Within coastal wetlands, herb‐dominated salt marshes had a significantly higher leaf P content, lower leaf N:P ratio and lower scaling exponent of leaf N to P than tree‐dominated mangroves.Main conclusionsThe similar latitudinal patterns of leaf stoichiometry in coastal wetlands compared with terrestrial ecosystems reflected the similar influences of temperature. However, different slopes of leaf P and N:P ratios and N and P scaling relationships between these two ecosystems suggested that different salinity and tidal inundation levels result in different strategies of N and P use in coastal wetland plants. These differences in leaf stoichiometry between ecosystems and between different types of coastal wetlands might need to be emphasized in future biogeochemical modelling owing to their different roles in global nutrient and carbon cycling.

From South Asia to the world: embracing the challenge of global sustainable nitrogen management

From South Asia to the world: embracing the challenge of global sustainable nitrogen management

The Possession of Coccoliths Fails to Deter Microzooplankton Grazers

Phytoplankton play a central role in the regulation of global carbon and nutrient cycles, forming the basis of the marine food webs. A group of biogeochemically important phytoplankton, the coccolithophores, produce calcium carbonate scales that have been hypothesized to deter or reduce grazing by microzooplankton. Here, a meta-analysis of mesocosm-based experiments demonstrates that calcification of the cosmopolitan coccolithophore, Emiliania huxleyi, fails to deter microzooplankton grazing. The median grazing to growth ratio for E. huxleyi (0.56 ± 0.40) was not significantly different among non-calcified nano- or picoeukaryotes (0.71 ± 0.31 and 0.55 ± 0.34, respectively). Additionally, the environmental concentration of E. huxleyi did not drive preferential grazing of non-calcified groups. These results strongly suggest that the possession of coccoliths does not provide E. huxleyi effective protection from microzooplankton grazing. Such indiscriminate consumption has implications for the dissolution and fate of CaCO3 in the ocean, and the evolution of coccoliths.

IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses.

Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections of their cellular hosts, viruses can reshape microbial community structure and drive global nutrient cycling. Over the past decade, viral sequences identified from genomes and metagenomes have provided an unprecedented view of viral genome diversity in nature. Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here, we present the third version of IMG/VR, composed of 18 373 cultivated and 2 314 329 uncultivated viral genomes (UViGs), nearly tripling the total number of sequences compared to the previous version. These clustered into 935 362 viral Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs in IMG/VR are now reported as single viral contigs, integrated proviruses or genome bins, and are annotated with a new standardized pipeline including genome quality estimation using CheckV, taxonomic classification reflecting the latest ICTV update, and expanded host taxonomy prediction. The new IMG/VR interface enables users to efficiently browse, search, and select UViGs based on genome features and/or sequence similarity. IMG/VR v3 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.

Drivers of tropical soil invertebrate community composition and richness across tropical secondary forests using DNA metasystematics

Tropical forests are fundamental ecosystems, essential for providing terrestrial primary productivity, global nutrient cycling, and biodiversity. Despite their importance, tropical forests are currently threatened by deforestation and associated activities. Moreover, tropical regions are now mostly represented by secondary forest regrowth, with half of the remaining tropical forests as secondary forest. Soil invertebrates are an important component to the functioning and biodiversity of these soil ecosystems. However, it remains unclear how these past land-use activities and subsequent secondary forest developments have altered the soil invertebrate communities and any potential ecological consequences associated with this. DNA metabarcoding offers an effective approach to rapidly monitor soil invertebrate communities under different land-use practices and within secondary forests. In this study, we used DNA metabarcoding to detect community-based patterns of soil invertebrate composition across a primary forest, a 23-year-old secondary forest, and a 33-year-old secondary forest and the associated soil environmental drivers of the soil invertebrate community structure in the Maquenque National Wildlife Refuge of Costa Rica (MNWR). We also used a species contribution analysis (SIMPER) to determine which soil invertebrate groups may be an indication of these soils reaching a pre-disturbed state such as a primary forest. We found that the soil invertebrate community composition at class, order, family, and ESV level were mostly significantly different across that habitats. We also found that the primary forest had a greater richness of soil invertebrates compared to the 23-year-old and 33-year-old secondary forest. Moreover, a redundancy analysis indicated that soil moisture influenced soil invertebrate community structure and explained up to 22% of the total variation observed in the community composition across the habitats; whereas soil invertebrate richness was structured by soil microbial biomass carbon (C) (Cmic) and explained up to 52% of the invertebrate richness across the primary and secondary forests. Lastly, the SIMPER analysis revealed that Naididae, Entomobryidae, and Elateridae could be important indicators of soil and forest recuperation in the MNWR. This study adds to the increasing evidence that soil invertebrates are intimately linked with the soil microbial biomass carbon (Cmic) and that even after 33 years of natural regrowth of a forest, these land use activities can still have persisting effects on the overall composition and richness of the soil invertebrate communities.