Microbial Cycling Research Articles

Microbial cycling contributes to the release of dissolved inorganic phosphate into the groundwater of floodplain aquifers

Little is known about biological processes controlling inorganic phosphate (PO4) in groundwater ecosystems. Here we present analyses of groundwater samples from the Hetao Basin, China that show an increasing contribution of microbial cycling to groundwater PO4 from oxic to anoxic conditions along a flow path with phosphate-bound oxygen isotopes (δ18OPO4). Under oxic conditions, although 25–47% of the dissolved PO4 inherited the initial source signal of igneous apatite, groundwater δ18OPO4 reflected a pronounced impact of intracellular enzymatic cycling. Under anoxic conditions, dissolved PO4 carried a nearly exclusive equilibrium isotope signal, which was probably due to (i) release of PO4 with an equilibrium δ18OPO4 from Fe(III) oxides, as a result of Fe(III) reduction in the presence of Fe(III)- and sulfate-reducing bacteria; and/or (ii) cumulative microbial cycling of dissolved PO4 with increasing groundwater residence time. Our study highlights that PO4 in groundwater is tightly microbially cycled under a wide range of redox conditions and microbial cycling contributes to the release of PO4 in groundwater.

Size-dependent influences of nano- and micro-plastics exposure on feeding, antioxidant systems, and organic sulfur compounds in ciliate Uronema marinum

Protozoa play a pivotal role in the microbial cycle, and ciliated protozoan grazing habits are associated with dimethyl sulfide (DMS) cycle. Many studies have explored the impacts of nanoplastics (NPs) and microplastics (MPs) on ecotoxicological effects of ciliates. However, limited research exists on NPs and MPs influences on the production of organic sulfur compounds. The impact of NPs and MPs on the production of dimethyl sulfoxide (DMSO) and carbonyl sulfide (COS) remains unclear. Therefore, we examined the impacts of three concentrations (1 × 105, 5 × 105, and 1 × 106 items/mL) of polystyrene (PS) NPs (50 nm) and MPs (1 and 5 μm) on the ecotoxicology and DMS/dimethylsulfoniopropionate (DMSP)/DMSO/COS production in the ciliate Uronema marinum. NPs and MPs exposure were found to reduce the abundance, growth rate, volume, and biomass of U. marinum. Additionally, NPs and MPs increased the superoxide anion radical (O2˙─) production rates and malondialdehyde (MDA) contents (24 h), leading to a decline in glutathione (GSH) content and an ascend in superoxide dismutase (SOD) activity to mitigate the effects of reactive oxygen species (ROS). Exposure to PS NPs and MPs decreased the ingestion rates of algae by 7.5–14.4%, resulting in decreases in DMS production by 56.8–85.4%, with no significant impact on DMSO production. The results suggest a distinct pathway for the production of DMSO or COS compared to DMS. These findings help us to understand the NPs and MPs impacts on the marine ecosystem and organic sulfur compound yield, potentially influencing the global climate.

Different effects of seasonal impoundment and land use change on microbiome in a tributary sediment of the three gorgers reservoir

Anthropogenic activities significantly impact river ecosystem nutrient fluxes and microbial metabolism. Here, we examined the seasonal and spatial variation of sediments physicochemical parameters and the associated microbiome in the Pengxi river, a representative tributary of Three Gorges Reservoir, in response to seasonal impoundment and land use change by human activities. Results revealed that seasonal impoundment and land use change enhanced total organic carbon (TOC), total nitrogen (TN) and ammonium nitrogen (NH4+-N) concentration in the sediment, but have different effects on sediment microbiome. Sediment microbiota showed higher similarity during the seasonal high-water level (HWL) in consecutive two years. The abundant phyla Acidobacteria, Gemmatimonadetes, Cyanobacteria, Actinobacteria and Planctomycetes significantly increased as water level increased. Along the changes in bacterial taxa, we also observed changes in predicted carbon fixation functions and nitrogen-related functions, including the significantly higher levels of Calvin cycle, 4HB/3HP cycle, 3HP cycle and assimilatory nitrate reduction, while significantly lower level of denitrification. Though land use change significantly increased TOC, TN and NH4+-N concentration, its effects on spatial variation of bacterial community composition and predicted functions was not significant. The finding indicates that TGR hydrologic changes and land use change have different influences on the carbon and nitrogen fluxes and their associated microbiome in TGR sediments. A focus of future research will be on assessing on carbon and nitrogen flux balance and the associated carbon and nitrogen microbial cycling in TGR sediment.

Genome-resolved metagenomics identifies novel active microbes in biogeochemical cycling within methanol-enriched soil.

Metagenome assembled genomes (MAGs), generated from sequenced 13C-labelled DNA from 13C-methanol enriched soils, were binned using an ensemble approach. This method produced a significantly larger number of higher-quality MAGs compared to direct binning approaches. These MAGs represent both the primary methanol utilizers and the secondary utilizers labelled via cross-feeding and predation on the labelled methylotrophs, including numerous uncultivated taxa. Analysis of these MAGs enabled the identification of multiple metabolic pathways within these active taxa that have climatic relevance relating to nitrogen, sulfur and trace gas metabolism. This includes denitrification, dissimilatory nitrate reduction to ammonium, ammonia oxidation and metabolism of organic sulfur species. The binning of viral sequence data also yielded extensive viral MAGs, identifying active viral replication by both lytic and lysogenic phages within the methanol-enriched soils. These MAGs represent a valuable resource for characterizing biogeochemical cycling within terrestrial environments.

Towards an integrated view on microbial CH4, N2O and N2 cycles in brackish coastal marsh soils: A comparative analysis of two sites

Coastal ecosystems, facing threats from global change and human activities like excessive nutrients, undergo alterations impacting their function and appearance. This study explores the intertwined microbial cycles of carbon (C) and nitrogen (N), encompassing methane (CH4), nitrous oxide (N2O), and nitrogen gas (N2) fluxes, to determine nutrient transformation processes between the soil-plant-atmosphere continuum in the coastal ecosystems with brackish water. Water salinity negatively impacted denitrification, bacterial nitrification, N fixation, and n-DAMO processes, but did not significantly affect archaeal nitrification, COMAMMOX, DNRA, and ANAMMOX processes in the N cycle. Plant species age and biomass influenced CH4 and N2O emissions. The highest CH4 emissions were from old Spartina and mixed Spartina and Scirpus sites, while Phragmites sites emitted the most N2O. Nitrification and incomplete denitrification mainly governed N2O emissions depending on the environmental conditions and plants. The higher genetic potential of ANAMMOX reduced excessive N by converting it to N2 in the sites with higher average temperatures. The presence of plants led to a decrease in the N fixers' abundance. Plant biomass negatively affected methanogenetic mcrA genes. Microbes involved in n-DAMO processes helped mitigate CH4 emissions. Over 93 % of the total climate forcing came from CH4 emissions, except for the Chinese bare site where the climate forcing was negative, and for Phragmites sites, where almost 60 % of the climate forcing came from N2O emissions. Our findings indicate that nutrient cycles, CH4, and N2O fluxes in soils are context-dependent and influenced by environmental factors and vegetation. This underscores the need for empirical analysis of both C and N cycles at various levels (soil-plant-atmosphere) to understand how habitats or plants affect nutrient cycles and greenhouse gas emissions.

Dimethyl Sulfide Emissions From a Peatland Result More From Organic Matter Degradation Than Sulfate Reduction

AbstractVolatile sulfur compounds (VSCs) contribute to acid rain, cloud formation, and albedo, and thus influence the climate. Their global emissions are quite uncertain, especially contributions from freshwater wetlands. We investigated the processes leading to hydrogen sulfide (H2S), methanethiol (MeSH), and dimethyl sulfide (Me2S) emissions in a slightly acidic peatland and found multiple indications that organic matter degradation rather than sulfate reduction is the main driver for Me2S emissions in this system. Evidence includes: the lack of labeled Me234S production after addition of Na234SO4 despite high emissions of Me34SH and H234S, and increased emission rates when soils were amended with organic substrates containing thiol groups (H2S emissions), methylthiols (MeSH), and dimethyl sulfonio groups (Me2S). VSC precursors were identified from an Untargeted Metabolomics data set from the same soil. The abundance of sulfur cycling microbes like Acidobacteria SD 1 and Desulfosporosinus correlated with VSC emissions. We conclude that organic matter degradation is more important than sulfate reduction as a source of Me2S in our peatland system, and potentially also in other organic and wetland soils.

氮磷添加下典型温带、亚热带森林土壤氮循环功能基因丰度和微生物群落属性数据集

Nitrogen (N) and phosphorus (P) are essential nutrients for soil microbial growth and activities. There are notable differences in the concentrations of N and P and the characteristics of microbial communities observed between temperate and subtropical forests soils, and this is also true for soil vertical profiles. As a consequence of the rise in global atmospheric N deposition, soil nutrient imbalances and P limitation are increasingly aggravated in eastern China. However, there is a lack of systematic dataset showing how N deposition and P addition affect soil N cycling microbes and soil physicochemical properties in eastern China; hence a comprehensive dataset is needed to a better understanding of the impact of N deposition and P addition on soil nitrogen cycle. This dataset is constructed based on the field experimental setup in the forests of Chinese Ecosystem Research Network (CERN). To obtain a systematic dataset on N-cycling microbial communities, we conducted measurements and collected data of soil N-cycling functional genes abundance, N-cycling microbial community diversities and compositions and enzyme activities in three typical forests with N and/or P additions. We collected 0-10 cm top soils from a temperate forest (Changbai Mountain) and two subtropical forests (Qianyanzhou and Dinghu Mountain) with field N and/or P additions, and the soils along 0-80 cm vertical profiles without nutrient additions. The N-cycling functional genes involved in the datasets cover ammonia oxidizing archaea amoA, ammonia oxidizing bacteria amoA, nirK, nirS, nosZ, qnorB, narG, nir, nifH and chiA. The potential activities included in the datasets cover nitrification activity, denitrification activity, nitrogen fixation activity and organic nitrogen decomposition enzyme activity. The datasets also include soil physiochemical properties, including soil pH, moisture content, N2O emission, net nitrification rate and the concentrations of organic carbon, NH4+ , NO3− , available phosphorus, total nitrogen, total carbon, total phosphorus and dissolved organic carbon. The creation and sharing of the datasets can provide data and support for understanding the microbial mechanisms of soil N-cycling and the modelling processes under the scenario of aggravated N deposition and P addition. The datasets will also provide support for forest management efforts with regard to greenhouse gas N2O emission, N and nutrient loss in forest ecosystems.

Effect of microplastic particles on the population growth rate and clearance rate of selected ciliates (Protista, Ciliophora).

Microplastics (MPs), due to their micro size, which overlaps with the typical food size of various aquatic organisms, can be ingested and move up the food chain, accumulating in the bodies of organisms at higher trophic levels. Few studies have focused on the uptake of MPs by ciliates, which are an important element of the microbial cycle. Three different ciliate species were used in this study: Blepharisma japonicum, Euplotes sp., and Spirostomum teres, as well as polystyrene beads with diameters of 1 and 2µm at two concentrations (106 and 107 beads × mL-1). The results of the experiments showed that MPs have a variable, species-specific effect on the population growth rate of ciliates, which is directly dependent on their concentration in the environment (P < 0.01). It was also observed that the number of MPs ingested changed over time depending on their concentration and size. On average, the highest number of ingested MPs (883.11 ± 521.47) was recorded at 60min of exposure to a low concentration of small beads in B. japonicum. The lowest number of beads was ingested after 5min of exposure to a low concentration of large beads in the same species. The rate of MP uptake by the ciliate species was significantly dependent on their concentration, exposure time, and size (P < 0.001). The highest clearance rate was observed in the fifth minute of the experiment in the environment with the lowest MP concentration.

The Response of Soil Bacterial Communities to Cropping Systems in Saline–Alkaline Soil in the Songnen Plain

The high salt content in saline–alkaline land leads to insufficient nutrients, thereby reducing agricultural productivity. This has sparked widespread interest in improving saline–alkaline soil. In this investigation, 16S rRNA gene high-throughput sequencing was employed to examine the impacts of three cropping systems (monoculture, rotation, and mixture) on soil bacterial communities. It was found that cropping rotations and mixtures significantly increased soil bacterial α-diversity. Random forest analysis showed a significant linear relationship between AK and EC and bacterial α-diversity. In addition, principal coordinates analysis (PCoA) further confirmed the significant differences in β-diversity between different soil layers. Through co-occurrence network analysis, it was found that cropping rotations and mixtures increased the stability and complexity of co-occurrence networks. By calculating NST to analyze the assembly process of soil bacterial communities in different cropping systems, it was found that the assembly process of soil bacterial communities was dominated by a stochastic process. Functional prediction results showed that a large number of C, N, and S cycling microbes appeared in soil bacterial communities. Our study aims to establish a fresh perspective on the improvement and recovery of saline–alkaline soil.

Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils.

Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria-methanotrophs and their respective traits.

Microbial interaction patterns and nitrogen cycling regularities in lake sediments under different trophic conditions

Exploring how nitrogen (N) cycling microbes interact in eutrophic lake sediments and how biogenic elements influence the nitrogen cycle is crucial for understanding biogeochemical cycles and nitrogen accumulation mechanisms. In this study, sediment samples were collected from various areas of Taihu Lake with different trophic conditions in all four seasons from 2015 to 2017. Using high-throughput sequencing and molecular ecological network analysis, we investigated the microbial interaction patterns and the role of nitrogen cycling in sediments from lakes with different trophic conditions. The results showed distinct structures of sediment microbial networks between lake areas with different trophic conditions. In the more eutrophic region, network indices indicate higher transfer efficiency of energy, material, and information, more significant competition, and weaker niche differentiation of the microbial community. The sedimentary environment in the moderately eutrophic area exhibited greater potential for denitrification, nitrification, and anammox compared to the mesotrophic area, but the inhibition between N functional microbes and limitations in N removal processes were also more likely to occur. The topological structure of the networks showed that the carbon (C), sulfur (S), and iron (Fe) cycles had a strong influence on the nitrogen cycle in both lake areas. In the moderately eutrophic lake area, C- and S-cycling functional bacteria facilitated a closed cycle of the coupled N fixation–nitrification–DNRA (dissimilatory nitrate reduction to ammonium) process and reduced N removal. In the mesotrophic lake area, C- and S-cycling functional bacteria promoted both N fixation and mineralization, and Fe-cycling functional bacteria coupled with denitrifiers enhanced the nitrogen removal process of products from nitrogen fixation and mineralization. This study improved the understanding of the nitrogen cycling mechanism in lake sediments under different trophic conditions.

Short-term perennial peanut integration into bahiagrass system influence on soil microbial-mediated nitrogen cycling activities and microbial co-occurrence networks

Integration of perennial peanuts into warm-season grasslands offers a potential solution to reduce nitrogen (N) fertilizer input and enhance N cycling through soil microbial activities. There is limited information on the changes in soil microbial diversity and communities following the short-term integration of rhizoma perennial peanut (RPP; Arachis glabrata Benth.) into warm-season perennial bahiagrass (Paspalum notatum Flüggé) as well as its impact on N cycling processes. This study investigated changes in N cycling populations and soil microbial communities in bahiagrass-RPP mixtures compared to their monocultures at <2 years after RPP establishment in Spring (March) and Fall (October) seasons. Real-time qPCR was used to quantity N functional groups in the soil involved in nitrification, denitrification, and N2 fixation. DNA amplicon sequencing was employed to examine co-occurrence networks of soil microbes, while activities of soil enzymes [N-Acetyl-β-d-glucosaminidase (NAG) and leucine aminopeptidase (LAP)] involved in N mineralization were also measured. Bahiagrass-RPP mixtures had no effect on N cycling genes. Ammonia oxidizing archaea were the major ammonia oxidizing prokaryotes compared to ammonia oxidizing bacteria in bahiagrass-RPP systems. We found that bahiagrass-RPP mixtures exhibited greater prokaryotic alpha diversity and NAG activities than RPP monoculture. Meanwhile, RPP influenced soil fungal community composition (beta diversity) and enhanced the relative abundance of dominant soil fungal genera (Fusarium, Gibberella, and Humicola). The presence of RPP in bahiagrass systems led to increased negative microbial interactions in microbial occurrence networks. Greater complexities in microbial networks were linked to forage growth season, which was related to enrichment of the relative abundance of Basidiomycota. Our findings showed that RPP has the potential to influence N cycling process in bahiagrass system by altering the abundance of certain N cycling microbes, especially fungal taxa, within 2 years of RPP establishment.

Clumped and conventional isotopes of natural gas reveal basin burial, denudation, and biodegradation history

Formation and post-genetic alteration of hydrocarbons provide insights into the dynamic and complex geologic, hydrologic, and microbial history of shallow crustal environments. Clumped isotopologues of methane (e.g., Δ13CH3D) have emerged as a proxy for constraining methane formation temperatures in sedimentary basins. However, unrealistically high apparent temperatures and microbial cycling of methane necessitate further investigation into how the generation and biodegradation of hydrocarbons may modify methane clumped isotopologue signatures. This study analyzed and modeled the clumped isotopologues of methane, in addition to traditional gas isotopes, to provide new insights into the origin, thermal maturity, migration, and biodegradation histories of hydrocarbons in the Paradox Basin in the Colorado Plateau. The basin was deeply buried in the geologic past and has been recently incised, leading to rapid denudation, enhanced meteoric circulation, and microbial activity. δ13CCH4 and CH4/ΣC2+ ratios suggest that most natural gases in various reservoirs throughout the basin are thermogenic in origin with variable thermal maturities. However, signatures suggestive of anaerobic oxidation of ethane and propane, and secondary microbial methane generation, exist. In the northeastern part of the basin, Δ13CH3D values in reservoirs above and below the Paradox Formation source rocks are consistent with thermodynamic equilibrium, indicating that the thermally mature hydrocarbons equilibrated at ≥160 °C during maximum burial over 30–80 Ma. Disequilibrium Δ13CH3D values of natural gas in Paradox Formation reservoirs along the southwestern margin of the basin suggest the presence of low-maturity hydrocarbons consistent with the region’s shallower burial history. Models of Δ13CH3D values based on the exchange rate of hydrogen isotopes between methane and water and the basin thermal history support that meteoric recharge and microbial activity, following incision/denudation over the past few million years, promoted anaerobic oxidation of hydrocarbons (particularly ethane and propane), biodegradation of crude oil, and generation of secondary microbial methane in shallow reservoirs.

The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival

BackgroundMicrobes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxsResultsHere we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival.ConclusionThe identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.

Highly active bacterial DMSP metabolism in the surface microlayer of the eastern China marginal seas.

The microbial cycling of dimethylsulfoniopropionate (DMSP) and the resulting gaseous catabolites dimethylsulfide (DMS) or methylmercaptan (MeSH) play key roles in the global sulfur cycle and potentially climate regulation. As the ocean-atmosphere boundary, the sea surface microlayer (SML) is important for the generation and emission of DMS and MeSH. However, understanding of the microbial DMSP metabolism remains limited in the SML. Here, we studied the spatiotemporal differences for DMS/DMSP, bacterial community structure and the key bacterial DMSP metabolic genes between SML and subsurface seawater (SSW) samples in the eastern China marginal seas (the East China Sea and Yellow Sea). In general, DMSPd and DMSPt concentrations, and the abundance of total, free-living and particle-associated bacteria were higher in SML than that in SSW. DMSP synthesis (~7.81-fold for dsyB, ~2.93-fold for mmtN) and degradation genes (~5.38-fold for dmdA, ~6.27-fold for dddP) detected in SML were more abundant compared with SSW samples. Free-living bacteria were the main DMSP producers and consumers in eastern Chinese marginal sea. Regionally, the bacterial community structure was distinct between the East China Sea and the Yellow Sea. The abundance of DMSP metabolic genes (dsyB, dmdA, and dddP) and genera in the East China Sea were higher than those of the Yellow Sea. Seasonally, DMSP/DMS level and DMSP metabolic genes and bacteria were more abundant in SML of the East China Sea in summer than in spring. Different from those in spring, Ruegeria was the dominant DMSP metabolic bacteria. In conclusion, the DMSP synthesis and degradation showed significant spatiotemporal differences in the SML of the eastern China marginal seas, and were consistently more active in the SML than in the SSW.

Moderate precipitation reduction enhances nitrogen cycling and soil nitrous oxide emissions in a semi-arid grassland.

The ongoing climate change is predicted to induce more weather extremes such as frequent drought and high-intensity precipitation events, causing more severe drying-rewetting cycles in soil. However, it remains largely unknown how these changes will affect soil nitrogen (N)-cycling microbes and the emissions of potent greenhouse gas nitrous oxide (N2 O). Utilizing a field precipitation manipulation in a semi-arid grassland on the Loess Plateau, we examined how precipitation reduction (ca. -30%) influenced soil N2 O and carbon dioxide (CO2 ) emissions in field, and in a complementary lab-incubation with simulated drying-rewetting cycles. Results obtained showed that precipitation reduction stimulated plant root turnover and N-cycling processes, enhancing soil N2 O and CO2 emissions in field, particularly after each rainfall event. Also, high-resolution isotopic analyses revealed that field soil N2 O emissions primarily originated from nitrification process. The incubation experiment further showed that in field soils under precipitation reduction, drying-rewetting stimulated N mineralization and ammonia-oxidizing bacteria in favor of genera Nitrosospira and Nitrosovibrio, increasing nitrification and N2 O emissions. These findings suggest that moderate precipitation reduction, accompanied with changes in drying-rewetting cycles under future precipitation scenarios, may enhance N cycling processes and soil N2 O emissions in semi-arid ecosystems, feeding positively back to the ongoing climate change.

Circadian rhythms of hosts and their gut microbiomes: Implications for animal physiology and ecology

Abstract Daily light–dark cycles shape the circadian physiology and behaviour of nearly all organisms, with variation in circadian phenotypes having cascading effects on individual fitness, species interactions and species co‐evolution. Recent evidence that circadian rhythms in host immunity and metabolism are synchronised by the gut microbiota suggest that the circadian dynamics of gut microbes are a crucial component of their function. However, there remains little knowledge or understanding of the diurnal dynamics of gut microbiomes in natural populations or the consequences for host physiology and ecology. Here, we summarise the hallmarks of gut microbiota oscillations reported to date and the mechanisms by which they synchronise rhythms in host immunity and metabolism. We outline the consequences for diverse biological processes such as host pathogen susceptibility and seasonal switches in metabolism, and discuss how the breakdown of these circadian interactions, for example during senescence or because of light pollution, may affect wildlife infection risk and disease. We also provide practical guidelines for the measurement of microbial oscillations in wildlife, highlighting that whilst faecal samples of wild animals are rarely available over a 24‐h period, characterising even parts of the gut microbial cycle can be informative. An improved understanding of how gut microbial diurnal rhythms manifest in wildlife is essential to fully comprehend their role in shaping variation in host circadian phenotypes and the consequences for host physiology and ecology. Read the free Plain Language Summary for this article on the Journal blog.

Mountaintop removal coal mining impacts on structural and functional indicators in Central Appalachian streams.

Mountaintop removal coal mining (MTR) has been a major source of landscape change in the Central Appalachians of the United States (US). Changes in stream hydrology, channel geomorphology and water quality caused by MTR coal mining can lead to severe impairment of stream ecological integrity. The objective of the Clean Water Act (CWA) is to restore and maintain the ecological integrity of the Nation's waters. Sensitive, readily measured indicators of ecosystem structure and function are needed for the assessment of stream ecological integrity. Most CWA assessments rely on structural indicators; inclusion of functional indicators could make these assessments more holistic and effective. The goals of this study were: (1) test the efficacy of selected carbon (C) and nitrogen (N) cycling and microbial structural and functional indicators for assessing MTR coal mining impacts on streams; (2) determine whether indicators respond to impacts in a predictable manner; and (3) determine if functional indicators are less likely to change than are structural indicators in response to stressors associated with MTR coal mining. The structural indicators are water quality and sediment organic matter concentrations, and the functional indicators relate to microbial activity and biofilm production. Seasonal measurements were conducted over the course of a year in streams draining small MTR-impacted and forested watersheds in the Twentymile Creek watershed of West Virginia (WV). Five of the eight structural parameters measured had significant responses, with all means greater in the MTR-impacted streams than in the forested streams. These responses resulted from changes in source or augmentation of the original source of the C and N structural parameters because of MTR coal mining. Nitrate concentration and the stable carbon isotopic ratio of dissolved inorganic carbon were the most effective indicators evaluated in this study. Only three of the fourteen functional indicators measured had significant responses to MTR coal mining, with all means greater in the forested streams than in the MTR-impacted streams. These results suggest that stressors associated with MTR coal mining caused reduction in some aspects of microbial cycling, but resource subsidies may have counterbalanced some of the inhibition leading to no observable change in most of the functional indicators. The detritus base, which is thought to confer functional stability, was likely sustained in the MTR-impacted streams by channel storage and/or leaf litter inputs from their largely intact riparian zones. Overall, our results largely support the hypothesis that certain functional processes are more resistant to stress induced change than structural properties but also suggest the difficulty of identifying suitable functional indicators for ecological integrity assessment.

Seasonal measurements of the nitrogenous osmolyte glycine betaine in marine temperate coastal waters

Glycine betaine (GBT) is a nitrogenous osmolyte ubiquitous throughout the marine environment. Despite its widespread occurrence and significance in microbial cycling, knowledge of the seasonality of this compound is lacking. Here, we present a seasonal dataset of GBT concentrations in marine suspended particulate material. Analysing coastal waters in the Western English Channel, GBT peaked in summer and autumn but did not follow the observed maxima in total phytoplankton biomass or chlorophyll a. Instead, we found evidence that GBT concentrations were associated with specific phytoplankton groups or species, particularly in the summer when GBT correlated with dinoflagellate biomass. In contrast, autumn maxima corresponded with a period of rapidly changing salinity and nutrient availability, with potential contributions from some phytoplankton species and Harpacticoid copepods. This suggests distinct environmental drivers for different periods of the GBT seasonality. Building on evidence that GBT and dinoflagellate biomass peak in summer, concomitantly with low nutrients, we propose that GBT positively affects dinoflagellate fitness, allowing them to outcompete other plankton when inorganic nutrients are depleted. By using this assumption, we improved the performance of a marine ecosystem model to reproduce the observed increase in dinoflagellates biomass in the transition from spring to summer. This work sheds light on the interplay between phytoplankton succession, competitive advantage and changing environmental factors relevant to climate change. It paves the way for future multidisciplinary research aiming to understand the importance of dinoflagellates in key coastal ecosystems and their potential significance for methylamine production, compounds relevant for particle growth in atmospheric chemistry.

Impacts of a subtropical storm on nitrogen functional microbes and associated cycling processes in a river-estuary continuum

Storms, in subtropical regions such as S.E. China, cause major changes in the physical and biogeochemical fluxes of anthropogenic N species through the river-estuary continuum to the coast. Two weeks continuous observations at a sampling station (Station E) in the upper Jiulong River Estuary (S.E. China) were conducted to track the changes of physical and biogeochemical parameters together with genomic identification of nitrogen cycling microbes through a complete storm event in June 2019. In conjunction with previous N flux measurements, it was found that there was greatly increased flux of N to and through the upper estuary during the storm. During the storm, the freshwater/brackish water boundary moved downstream, and previously deposited organic rich sediment was resuspended. During baseflow, anthropogenically derived ammonium was oxidised dominantly by the marine nitrifying (AOA) microbe Nitrosopelagicus. However, during the storm, the dominant ammonia-oxidizing archaea (AOA) at Station E changed to the riverine genus (Nitrosotenuis) while the marine genus, Nitrosopumilus decreased. At the same time the dominant ammonia-oxidizing bacteria (AOB) was still the marine genus (Nitrosomanas). Estuarine nitrifiers had higher abundance, weighted entropy and diversity during the Flood, suggesting that the high NH4-N and DO during the Rising period of the Flood resulted in a bloom of nitrifiers. The changing gene abundances of nitrifiers were reflected in changes in the concentration and isotopic composition of DIN confirming active nitrification in the oxygen-rich water column. During the storm the numbers of denitrifiers (narG, nirS and nod), DNRA (nrfA) and anammox (hzsB) were found in the water column increased, and the larger fraction was associated with the <22 μm free-living fraction. However it was not possible with the data obtained to estimate what fraction of these anaerobic bacteria were active in the dominantly oxic water column.