Abundance In Response Research Articles

Heat stress impacts the multi-domain ruminal microbiota and some of the functional features independent of its effect on feed intake in lactating dairy cows

BackgroundHeat stress (HS) affects the ruminal microbiota and decreases the lactation performance of dairy cows. Because HS decreases feed intake, the results of previous studies were confounded by the effect of HS on feed intake. This study examined the direct effect of HS on the ruminal microbiota using lactating Holstein cows that were pair-fed and housed in environmental chambers in a 2 × 2 crossover design. The cows were pair-fed the same amount of identical total mixed ration to eliminate the effect of feed or feed intake. The composition and structure of the microbiota of prokaryotes, fungi, and protozoa were analyzed using metataxonomics and compared between two thermal conditions: pair-fed thermoneutrality (PFTN, thermal humidity index: 65.5) and HS (87.2 for daytime and 81.8 for nighttime).ResultsThe HS conditions altered the structure of the prokaryotic microbiota and the protozoal microbiota, but not the fungal microbiota. Heat stress significantly increased the relative abundance of Bacteroidetes (primarily Gram-negative bacteria) while decreasing that of Firmicutes (primarily Gram-positive bacteria) and the Firmicutes-to-Bacteroidetes ratio. Some genera were exclusively found in the heat-stressed cows and thermal control cows. Some co-occurrence and mutual exclusion between some genera were also found exclusively for each thermal condition. Heat stress did not significantly affect the overall functional features predicted using the 16S rRNA gene sequences and ITS1 sequences, but some enzyme-coding genes altered their relative abundance in response to HS.ConclusionsOverall, HS affected the prokaryotes, fungi, and protozoa of the ruminal microbiota in lactating Holstein cows to a different extent, but the effect on the structure of ruminal microbiota and functional profiles was limited when not confounded by the effect on feed intake. However, some genera and co-occurrence were exclusively found in the rumen of heat-stressed cows. These effects should be attributed to the direct effect of heat stress on the host metabolism, physiology, and behavior. Some of the “heat-stress resistant” microbes may be useful as potential probiotics for cows under heat stress.

Soil microbial nitrogen-cycling gene abundances in response to crop diversification: A meta-analysis

Single planting structure has a significant impact on the maintenance of nitrogen in managed ecosystems. Although the effect of crop diversity on soil nitrogen-cycling microbes is mainly related to the influence of environmental factors, there is a lack of quantitative research. This study aims to determine the effect of diversified cropping mode on the abundance of functional genes in the soil nitrogen cycle based on the quantitative integration of a meta-analysis database containing 189 observation data pairs. The results show that the soil nifH (nitrogenase coding gene), nirS and nirK (nitrite reductase coding gene), and narG (nitrate reductase coding gene) abundances are positively affected by the diversity of plant species, whereas the amoA (ammonia monooxygenase coding gene) and nosZ (nitrous oxide reductase coding gene) show no response. Diversification duration and ecosystem type are important factors that regulate soil nitrogen fixation and nitrification gene abundances. Denitrification genes are mainly affected by categorical variables such as the planting pattern, soil layer, application species, duration, and soil texture. Among them, the long-term continuous diversification is mainly manifested in the reduction of soil nifH and increase of nirK abundances. Soil organic carbon and nitrogen linearly affect the responses of nifH, amoA, nirS, and nirK. Therefore, to maintain the soil ecological function, diversity of planting patterns needs to be applied flexibly by regulating the abundance of nitrogen-cycling genes. Our study draws conclusions in order to provide theoretical references for the sustainability of nitrogen and improvement of management measures in the process of terrestrial managed ecosystem diversification.

A 15-year monitoring of Rickettsiales (Anaplasma phagocytophilum and Rickettsia spp.) in questing ticks in the city of Hanover, Germany

Rickettsiales (Anaplasma phagocytophilum and Rickettsia spp.) are regarded as potentially emerging tick-borne pathogens and may change in abundance in response to global climate change. However, continuous monitoring on their prevalence in questing ticks is only available for the northern German city of Hanover. In the presented follow-up of this long-term study, 2100 questing ticks of the Ixodes ricinus/Ixodes inopinatus-complex collected from April to October 2020 at ten different recreation sites in Hanover were individually analysed for Rickettsia and A. phagocytophilum infection by quantitative real-time PCR. Together with previous results from years 2005, 2010 and 2015, the current study allows to assess potential changes in tick infection rates with Rickettsiales over a 15-year monitoring period. In 2020, 3.0% (63/2100) of ticks were infected with A. phagocytophilum, 36.0% (756/2100) with Rickettsia spp. and 1.2% (26/2100) with both pathogens. Regarding the different developmental tick stages, nymphs showed a significantly lower A. phagocytophilum prevalence of 0.5% (5/1050) than adult ticks (5.5% [58/1050]) as well as compared to females (5.4% [38/700]) and males (5.7% [20/350]). For Rickettsia spp., nymphs also showed a lower prevalence of 33.2% (349/1050) with a significant difference to adult ticks (38.8% [407/1050]) and female ticks (40.7% [285/700]), while males had a Rickettsia infection rate of 34.9% (122/350). Comparison with previous years indicated a stable A. phagocytophilum prevalence over the 15-year monitoring period. In contrast, fluctuating Rickettsia prevalences were observed, with a peak in 2015 in all developmental stages, but similar infection rates in 2005 and 2020. Therefore, epidemiological changes in response to climate change are not (yet) evident. Nevertheless, the long-term monitoring study will be continued in the future, as climatic impacts on tick and reservoir host populations may have a delayed effect on pathogen prevalence and, consequently, transmission to humans and domestic animals.

StaRTrEK:in silico estimation of RNA half-lives from genome-wide time-course experiments without transcriptional inhibition

BackgroundGene expression is the result of the balance between transcription and degradation. Recent experimental findings have shown fine and specific regulation of RNA degradation and the presence of various molecular machinery purposely devoted to this task, such as RNA binding proteins, non-coding RNAs, etc. A biological process can be studied by measuring time-courses of RNA abundance in response of internal and/or external stimuli, using recent technologies, such as the microarrays or the Next Generation Sequencing devices. Unfortunately, the picture provided by looking only at the transcriptome abundance may not gain insight into its dynamic regulation. By contrast, independent simultaneous measurement of RNA expression and half-lives could provide such valuable additional insight. A computational approach to the estimation of RNAs half-lives from RNA expression time profiles data, can be a low-cost alternative to its experimental measurement which may be also affected by various artifacts.ResultsHere we present a computational methodology, called StaRTrEK (STAbility Rates ThRough Expression Kinetics), able to estimate half-life values basing only on genome-wide gene expression time series without transcriptional inhibition. The StaRTrEK algorithm makes use of a simple first order kinetic model and of a l_1-norm regularized least square optimization approach to find its parameter values. Estimates provided by StaRTrEK are validated using simulated data and three independent experimental datasets of two short (6 samples) and one long (48 samples) time-courses.ConclusionsWe believe that our algorithm can be used as a fast valuable computational complement to time-course experimental gene expression studies by adding a relevant kinetic property, i.e. the RNA half-life, with a strong biological interpretation, thus providing a dynamic picture of what is going in a cell during the biological process under study.

Does G protein‐coupled Estrogen Receptor 1 Contribute to Cisplatin‐induced Acute Kidney Injury?

Cisplatin (Cp) is an effective chemotherapeutic agent used to treat a wide variety of malignancies. Nephrotoxicity is the dose‐limiting side effect of Cp. Acute kidney injury (AKI) following Cp administration is multi‐factorial, involving cellular toxicity, inflammation and proximal tubular injury. Recent evidence points to renal protective actions of G protein‐coupled estrogen receptor 1 (GPER1) in nephropathies evoked by salt loading, hypertension, methotrexate and ischemia reperfusion. Additionally, GPER1 abundance increases after renal ischemia reperfusion injury. However, the involvement of GPER1 signaling in Cp‐induced nephrotoxicity remains unclear. Therefore, this study was designed to test whether genetic deletion of GPER1 exacerbates Cp‐induced AKI in male mice. We subjected 14‐16 weeks‐old male mice homozygous (homo), heterozygous (het) for GPER1 gene and wild‐type (WT) littermates to Cp or saline injections and assessed markers for renal injury on the third day after injections. Specifically, we measured serum creatinine (sCr), urea, neutrophil gelatinase‐associated lipocalin (NGAL), histological indexes of renal tubular injury and abundance of kidney injury molecule‐1 (KIM‐1) and NGAL in the kidney. We determined also serum levels of proinflammatory markers in saline and Cp‐treated mice. A rise sCr was evident in all Cp‐treated mice, compared to saline‐treated mice (WT: 1.72±0.24 vs. 0.12±0.01; het: 1.14±0.30 vs. 0.12±0.01; homo: 1.28±0.31 vs. 0.14±0.01 mg/dl, p<0.0001, p=0.0149, p=0.0028, respectively, n=9‐13). Serum urea and NGAL levels followed the same pattern as sCr. Cp‐induced AKI resulted in comparable histological evidence of injury in all genotypes. Kidney KIM‐1 abundance was higher in saline‐treated homo mice, compared to corresponding WT mice (14.00±2.30 vs. 7.62±0.70 AU, respectively, p=0.0188, n=8, 13). Kidney KIM‐1 abundance was markedly upregulated in response to Cp in all groups, however, no genotypic differences were observed in kidney KIM‐1 in Cp‐treated mice. Cytokine panel assessment demonstrated increased circulating levels of interleukin‐2 (IL‐2), IL‐5, IL‐10 and tumor necrosis factor‐a in Cp‐treated mice. GPER1 deletion lowered plasma IL‐12p70 (p=0.0176). Given the protective role of heme oxygenase‐1 (HO‐1) in Cp‐mediated cell injury, we also investigated genotypic differences in renal HO‐1 abundance. WT and homo mice showed greater renal HO‐1 abundance in response to Cp. Interestingly, renal HO‐1 abundance was lower in Cp‐treated homo, compared to Cp‐treated WT mice (65.74±6.70 vs. 87.83±5.11 AU, respectively, p=0.0083, n=8, 13), despite the lack of genotypic differences in kidney HO‐1 levels in saline‐treated mice. Overall, we demonstrate that GPER1 homo, het male mice and WT littermates elicit comparable renal injury in response to Cp. We show also that GPER1 deletion diminishes HO‐1 induction in response Cp, suggesting that GPER1 may play a permissive role for HO‐1 cytoprotective actions in AKI. GPER1‐induced regulation of HO‐1 after Cp treatment may offer a novel therapeutic target for the treatment of AKI.

Antioxidant Metabolism Underlies Different Metabolic Strategies for Primary Root Growth Maintenance under Water Stress in Cotton and Maize.

The divergence of metabolic responses to water stress in the elongation zone of cotton and maize primary roots was investigated by establishing water-deficit conditions that generated steady root elongation at equivalent tissue water potentials. In water-stressed cotton roots, cell elongation was maintained in the apical 3 mm but was progressively inhibited with further displacement from the apex. These responses are similar to previous findings in maize, providing the foundation for comparisons of metabolic responses in regions of growth maintenance and inhibition between the species. Metabolomics analyses showed region-specific and species-specific changes in metabolite abundance in response to water stress, revealing both conserved responses including osmolyte accumulation, and key differences in antioxidative and sulfur metabolism. Quantitative assessment showed contrasting glutathione responses in the root elongation zone between the species, with glutathione levels declining in cotton as stress duration progressed, whereas in maize, glutathione levels remained elevated. Despite the lesser glutathione response in cotton, hydrogen peroxide levels were low in water-stressed cotton compared with maize roots and were associated with higher catalase, ascorbate peroxidase, and superoxide dismutase activities in cotton. The results indicate alternative metabolic strategies underlying the responses of primary root growth to water stress between cotton and maize.

A dietary carbohydrate – gut Parasutterella – human fatty acid biosynthesis metabolic axis in obesity and type 2 diabetes

ABSTRACT Recent rodent microbiome experiments suggest that besides Akkermansia, Parasutterella sp. are important in type 2 diabetes and obesity development. In the present translational human study, we aimed to characterize Parasutterella in our European cross-sectional FoCus cohort (n = 1,544) followed by validation of the major results in an independent Canadian cohort (n = 438). In addition, we examined Parasutterella abundance in response to a weight loss intervention (n = 55). Parasutterella was positively associated with BMI and type 2 diabetes independently of the reduced microbiome α/β diversity and low-grade inflammation commonly found in obesity. Nutritional analysis revealed a positive association with the dietary intake of carbohydrates but not with fat or protein consumption. Out of 126 serum metabolites differentially detectable by untargeted HPLC-based MS-metabolomics, L-cysteine showed the strongest reduction in subjects with high Parasutterella abundance. This is of interest, since Parasutterella is a known high L-cysteine consumer and L-cysteine is known to improve blood glucose levels in rodents. Furthermore, metabolic network enrichment analysis identified an association of high Parasutterella abundance with the activation of the human fatty acid biosynthesis pathway suggesting a mechanism for body weight gain. This is supported by a significant reduction of the Parasutterella abundance during our weight loss intervention. Together, these data indicate a role for Parasutterella in human type 2 diabetes and obesity, whereby the link to L-cysteine might be relevant in type 2 diabetes development and the link to the fatty acid biosynthesis pathway for body weight gain in response to a carbohydrate-rich diet in obesity development.

Coordination Between Phloem Loading and Structure Maintains Carbon Transport Under Drought.

Maintaining phloem transport under water stress is expected to be crucial to whole-plant drought tolerance, but the traits that benefit phloem function under drought are poorly understood. Nearly half of surveyed angiosperm species, including important crops, use sucrose transporter proteins to actively load sugar into the phloem. Plants can alter transporter abundance in response to stress, providing a potential mechanism for active-loading species to closely regulate phloem loading rates to avoid drought-induced reductions or failures in phloem transport. We developed an integrated xylem-phloem-stomatal model to test this hypothesis by quantifying the joint impacts of transporter kinetics, phloem anatomy, and plant water status on sucrose export to sinks. We parameterized the model with phloem hydraulic resistances and sucrose transporter kinetic parameters compiled from the literature, and simulated loading regulation by allowing loading rates to decline exponentially with phloem pressure to prevent excessive sucrose concentrations from inducing viscosity limitations. In the absence of loading regulation, where loading rates were independent of phloem pressure, most resistance values produced unrealistic phloem pressures owing to viscosity effects, even under well-watered conditions. Conversely, pressure-regulated loading helped to control viscosity buildup and improved export to sinks for both lower and higher resistant phloem pathways, while maintaining realistic phloem pressures. Regulation also allowed for rapid loading and export in wet conditions while maintaining export and viable phloem pressures during drought. Therefore, we expect feedbacks between phloem pressure and loading to be critical to carbon transport in active-loading species, especially under drought, and for transporter kinetics to be strongly coordinated with phloem architecture and plant water status. This work provides an important and underexplored physiological framework to understand the ecophysiology of phloem transport under drought and to enhance the genetic engineering of crop plants.

GCgx: transcriptome-wide exploration of the response to glucocorticoids.

Glucocorticoids are the cornerstone of immunosuppressive and anti-inflammatory therapy in humans, yet the mechanisms of glucocorticoid immunoregulation and toxicity remain unclear. The response to glucocorticoids is highly cell type-dependent, so translating results from different experimental systems into a better understanding of glucocorticoid effects in humans would benefit from rapid access to high-quality data on the response to glucocorticoids by different cell types. We introduce GCgx, a web application that allows investigators to quickly visualize changes in transcript abundance in response to glucocorticoids in a variety of cells and species. The tool is designed to grow by the addition of datasets based on input from the user community. GCgx is implemented in R and HTML and packaged as a Docker image. The tool and its source code are publicly available.

POS-338 PEROXISOMAL DYSFUNCTION AND REDUCED PEXOPHAGY PROMOTES PROXIMAL TUBULES CELL INJURY IN DIABETIC NEPHROPATHY

Peroxisomes are highly dynamic, changing in abundance in response to metabolic stress which present in many kinds of cells especially in liver cells and kidney cells. Peroxisomal homeostasis is regulated by a delicate balance between the formation of new peroxisomes and autophagic degradation of existing peroxisomes (pexophagy). Pexophagy dysregulation are linked to many neurological disorders, especially peroxisome biogenesis disorders (PBDs). However, our understanding of peroxisomes’ roles in diabetic nephropathy is still unclear.

Using Proteomic Approaches to Unravel the Response of Ctenocephalides felis felis to Blood Feeding and Infection With Bartonella henselae.

Among the Ctenocephalides felis felis-borne pathogens, Bartonella henselae, the main aetiological agent of cat scratch disease (CSD), is of increasing comparative biomedical importance. Despite the importance of B. henselae as an emergent pathogen, prevention of the diseases caused by this agent in cats, dogs and humans mostly relies on the use of ectoparasiticides. A vaccine targeting both flea fitness and pathogen competence is an attractive choice requiring the identification of flea proteins/metabolites with a dual effect. Even though recent developments in vector and pathogen -omics have advanced the understanding of the genetic factors and molecular pathways involved at the tick-pathogen interface, leading to discovery of candidate protective antigens, only a few studies have focused on the interaction between fleas and flea-borne pathogens. Taking into account the period of time needed for B. henselae replication in flea digestive tract, the present study investigated flea-differentially abundant proteins (FDAP) in unfed fleas, fleas fed on uninfected cats, and fleas fed on B. henselae-infected cats at 24 hours and 9 days after the beginning of blood feeding. Proteomics approaches were designed and implemented to interrogate differentially expressed proteins, so as to gain a better understanding of proteomic changes associated with the initial B. henselae transmission period (24 hour timepoint) and a subsequent time point 9 days after blood ingestion and flea infection. As a result, serine proteases, ribosomal proteins, proteasome subunit α-type, juvenile hormone epoxide hydrolase 1, vitellogenin C, allantoinase, phosphoenolpyruvate carboxykinase, succinic semialdehyde dehydrogenase, glycinamide ribotide transformylase, secreted salivary acid phosphatase had high abundance in response of C. felis blood feeding and/or infection by B. henselae. In contrast, high abundance of serpin-1, arginine kinase, ribosomal proteins, peritrophin-like protein, and FS-H/FSI antigen family member 3 was strongly associated with unfed cat fleas. Findings from this study provide insights into proteomic response of cat fleas to B. henselae infected and uninfected blood meal, as well as C. felis response to invading B. henselae over an infection time course, thus helping understand the complex interactions between cat fleas and B. henselae at protein levels.

Eosinophils regulate intra-adipose axonal plasticity.

Sympathetic innervation regulates energy balance, and the nerve density in the adipose tissues changes under various metabolic states, resulting in altered neuronal control and conferring resilience to metabolic challenges. However, the impact of the immune milieu on neuronal innervation is not known. Here, we examined the regulatory role on nerve plasticity by eosinophils and found they increased cell abundance in response to cold and produced nerve growth factor (NGF) in the white adipose tissues (WAT). Deletion of Ngf from eosinophils or depletion of eosinophils impairs cold-induced axonal outgrowth and beiging process. The spatial proximity between sympathetic nerves, IL-33-expressing stromal cells, and eosinophils was visualized in both human and mouse adipose tissues. At the cellular level, the sympathetic adrenergic signal induced calcium flux in the stromal cells and subsequent release of IL-33, which drove the up-regulation of IL-5 from group 2 innate lymphoid cells (ILC2s), leading to eosinophil accretion. We propose a feed-forward loop between sympathetic activity and type 2 immunity that coordinately enhances sympathetic innervation and promotes energy expenditure.

Receptor control by membrane-tethered ubiquitin ligases in development and tissue homeostasis.

Paracrine cell-cell communication is central to all developmental processes, ranging from cell diversification to patterning and morphogenesis. Precise calibration of signaling strength is essential for the fidelity of tissue formation during embryogenesis and tissue maintenance in adults. Membrane-tethered ubiquitin ligases can control the sensitivity of target cells to secreted ligands by regulating the abundance of signaling receptors at the cell surface. We discuss two examples of this emerging concept in signaling: (1) the transmembrane ubiquitin ligases ZNRF3 and RNF43 that regulate WNT and bone morphogenetic protein receptor abundance in response to R-spondin ligands and (2) the membrane-recruited ubiquitin ligase MGRN1 that controls Hedgehog and melanocortin receptor abundance. We focus on the mechanistic logic of these systems, illustrated by structural and protein interaction models enabled by AlphaFold. We suggest that membrane-tethered ubiquitin ligases play a widespread role in remodeling the cell surface proteome to control responses to extracellular ligands in diverse biological processes.

Proteomic Response of Deinococcus radiodurans to Short-Term Real Microgravity during Parabolic Flight Reveals Altered Abundance of Proteins Involved in Stress Response and Cell Envelope Functions.

Rapidly evolving space exploration makes understanding the short- and long- term effects of microgravity on humans, plants, and microorganisms an important task. The ubiquitous presence of the gravitational force has had an influence on the development of all living entities on Earth, and short- and long-term changes in perceived gravitational force can induce notable changes within cells. Deinococcus radiodurans is the Gram-positive bacterium that is best known for its extreme resistance to UV-C and gamma radiation, oxidation stress, and desiccation. Thus increased interest has been placed on this species in the context of space research. The present study aims to elucidate the short-term proteomic response of this species to real microgravity during parabolic flight. Overnight cultures of D. radiodurans were subjected to microgravity during a single parabola, and metabolic activity was quenched using methanol. Proteins were extracted and subsequently measured using HPLC nESI MS/MS. The results, such as the enrichment of the peptidoglycan biosynthesis pathway with differentially abundant proteins and altered S-layer protein abundance, suggested molecular rearrangements in the cell envelope of D. radiodurans. Altered abundance of proteins involved in energy metabolism and DNA repair could be linked with increased endogenous ROS production that contributes to the stress response. Moreover, changes in protein abundance in response to microgravity show similarities with previously reported stress responses. Thus, the present results could be used to further investigate the complex regulation of the remarkable stress management of this bacterium.

Quantitative proteomic analysis of Neosartorya pseudofischeri ascospores subjected to heat treatment

Neosartorya pseudofischeri, a heat- resistant fungus, was isolated from contaminated blueberry juice in our laboratory. To obtain a better understanding of the cellular process of heat- resistant fungus, a quantitative proteomic investigation employing stable isotope labeling by peptide demethylation was conducted on changes in intracellular proteins of N. pseudofischeri ascospores subjected to heat treatment at 93 °C for 0, 1 or 8 min. In total, 811 proteins were identified and quantified. Using the normalized ratio of protein abundance, proteins that changed more than two- fold after heat treatment were identified as significantly increased or decreased proteins and grouped into four clusters based on their quantitative changes. Decreased proteins were found mainly involved in the central carbon metabolism, heat stress responses, reactive oxygen intermediates elimination and translation events. A group of proteins in relation to toxicant degradation and antibiotic neutralization linking to environmental adaptability and tolerance of heat- resistant, was also identified. These findings provide insights into protein changes of N. pseudofischeri ascospores and lay foundations for further investigations on heat- resistant molds using targeted quantitative approaches. Significance of the researchHeat- resistant fungi can survive pasteurization processes, and subsequently germinate and grow to cause spoilage of food products, leading to significant economic losses for the food industry and potential health risk for the consumers.To obtain a better understanding of the cellular process of heat- resistant fungi, a quantitative proteomic approach employing stable isotope labeling by peptide demethylation has been used to investigate the intracellular protein changes of N. pseudofischeri ascospores isolated from blueberry juice and subjected to heat treatment. 150 significantly changed proteins were grouped into four clusters based on their quantitative changes. The significant decrease in protein abundance in response to heat treatment revealed possible mechanism that N. pseudofischeri ascospores could survive the heat treatment.This is the first proteomic profile report for N. pseudofischeri. These findings provide insights into protein changes of N. pseudofischeri and lay foundations for further investigations on heat- resistant fungi using targeted quantitative approaches to evaluate the efficiency of thermal treatment for processed food products.

Changes in precipitation regime lead to acceleration of the N cycle and dramatic N2O emission

Alpine meadows on the Qinghai-Tibetan Plateau are sensitive to climate change. The precipitation regime in this region has undergone major changes, “repackaging” precipitation from more frequent, smaller events to less frequent, larger events. Nitrous oxide (N2O) is an important indicator of responses to global change in alpine meadow ecosystems. However, little information is available describing the mechanisms driving the response of N2O emissions to changes in the precipitation regime. In this study, a manipulative field experiment was conducted to investigate N2O flux, soil properties, enzyme activity, and gene abundance in response to severe and moderate changes in precipitation regime over two years. Severe changes in precipitation regime led to a 12.6-fold increase in N2O fluxes (0.0068 ± 0.0018 mg m−2 h−1) from Zoige alpine meadows relative to natural conditions (0.0005 ± 0.0029 mg m−2 h−1). In addition, severe changes in precipitation regime significantly suppressed the activities of leucine amino peptidase (LAP) and peroxidase (PEO), affected ecoenzymatic stoichiometry, and increased the abundances of gdhA, narI and nirK genes, which significantly promoted organic nitrogen (N) decomposition, denitrification, and anammox processes. The increase in abundance of these genes could be ascribed to changes in the abundance of several dominant bacterial taxa (i.e., Actinobacteria and Proteobacteria) as a result of the altered precipitation regime. Decreases in nitrate and soil moisture caused by severe changes in precipitation may exacerbate N limitation and water deficit, lead to a suppression of soil enzyme activity, and change the structure of microorganism community. The N cycle of the alpine meadow ecosystem may accelerate by increasing the abundance of key N functional genes. This would, in turn, lead to increased N2O emission. This study provided insights into how precipitation regimes changes affect N cycling, and may also improve prediction of N2O fluxes in response to changes in precipitation regime.

Soil enzymes illustrate the effects of alder nitrogen fixation on soil carbon processes in arctic and boreal ecosystems

AbstractAs tall shrubs increase in extent and abundance in response to a changing climate, they have the potential to substantially alter Arctic and boreal ecosystem nutrient cycling and carbon (C) balance. Siberian alder (Alnus viridisssp.fruticosa), a nitrogen (N) fixing shrub, is among the species responding to climate warming in both the Arctic and boreal forests. By relieving N limitation of microbial activity, alder‐fixed N has the potential to increase decomposition of labile soil C. Simultaneously, it may also decrease decomposition of recalcitrant soil C by downregulating microbial N mining. The microbial response to N additions is influenced by differences in the soil organic matter (SOM) chemistry and could ultimately determine whether alder N additions result in a net sink or source of C to the atmosphere. We measured the activities of three extracellular enzymes in bulk organic soils under and away from alder canopies in stands differing in SOM chemistry in both the arctic and boreal forest regions of Alaska, USA. In the Arctic, samples taken from under alder had higher activities of both recalcitrant and labile C‐degrading enzymes than samples taken away, regardless of SOM chemistry. In the boreal forest, enzyme activities did not differ with alder proximity nor stand SOM chemistry, possibly due to long legacies of alder N inputs in these stands. As arctic and boreal forest ecosystems experience shifts in the distribution and abundance of this N‐fixing shrub, alders' influence on soil decomposition could have significant consequences for high latitude soil C budgets.

Increased grazing drives homogenisation but reduced grazing increases turnover in upland habitat mosaics

Many ecosystems are grazed by livestock or large, wild herbivores and exist as mosaics of different vegetation communities. Changing grazing could have an impact on heterogeneity as well as on composition. A long-term, large-scale grazing experiment that maintained existing low-intensity sheep grazing, tripled it, removed it and partially substituted sheep grazing by cattle grazing was set up on a mosaic of upland vegetation types. The impact of changing grazing regimes was assessed in terms of changes in temporal and spatial species and functional beta diversity. Removal of grazing had the highest impact on species replacement, whilst increased grazing was closest to maintaining the original species complement. Wet heath and Molina mire had the lowest turnover, but wet heath showed the highest changes in unidirectional abundance as it contained species capable of increasing in abundance in response to changing grazing intensity. Agrostis-Festuca and Nardus grasslands displayed the highest level of balanced species replacement reflecting their more dynamic vegetation. In functional terms, there was no clear separation of communities based on their grazing preference, all were relatively resistant to change but Nardus grassland was the most resistant to the removal of grazing. The increased offtake associated with increased grazing led to a degree of homogenisation as grazing tolerant species associated with preferred communities increased in the unpreferred ones. Decisions about grazing management of the uplands involve many trade-offs, and this study identified potential trade-offs between stability and homogenisation to add to existing ones on the biodiversity of different groups of species and on ecosystem services.

Waterbird diversity and abundance in response to variations in climate in the Liaohe Estuary, China

Birds are sensitive to environmental change and thus good indicators of biodiversity and ecosystem health. Because birds fill a variety of functional roles, understanding their diversity patterns is important to inform and support conservation management. This study focused on the diversity and abundance of waterbirds occupying the Liaohe Estuary, an internationally important habitat, and migratory stopover in northeast China. Analyzing data from 42 monitoring stations/transects collected over ten years, we determined the seasonal abundance and distribution of waterbirds throughout the estuary and surrounding lands and looked for associations with climatic data shown to influence bird populations. Results showed that although global populations of waterbirds are decreasing, bird abundance, richness, and alpha diversity increased in the Liaohe Estuary during our 10- year study. Distinct annual patterns of species distribution were detected during spring and autumn with population lower in spring than autumn. Analyses with non-metric multidimensional scaling (NMS) showed that spring populations had a strong and positive relationship to temperature variables including spring mean temperature and cumulative temperature days. There was a clear distribution of waterbird species along the axis of the spring temperature range and precipitation. Whereas in autumn, waterbird populations had a strong and negative relationship to precipitation variables including annual precipitation, autumn precipitation, and autumn maximum precipitation. These findings indicate that waterbird diversity in this region and others may be responsive to climate change, especially in spring season. We discuss the ramifications of these shifts in terms of future utilization of the estuary by waterbirds in the region. We project that as temperatures continue to warm and precipitation decreases, there may be increasing migratory stopover and breeding in the Liaohe Estuary and thus populations may continue to increase in the future.

A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms

Increasing occurrence of harmful algal blooms across the land–water interface poses significant risks to coastal ecosystem structure and human health. Defining significant drivers and their interactive impacts on blooms allows for more effective analysis and identification of specific conditions supporting phytoplankton growth. A novel iterative Random Forests (iRF) machine-learning model was developed and applied to two example cases along the California coast to identify key stable interactions: (1) phytoplankton abundance in response to various drivers due to coastal conditions and land-sea nutrient fluxes, (2) microbial community structure during algal blooms. In Example 1, watershed derived nutrients were identified as the least significant interacting variable associated with Monterey Bay phytoplankton abundance. In Example 2, through iRF analysis of field-based 16S OTU bacterial community and algae datasets, we independently found stable interactions of prokaryote abundance patterns associated with phytoplankton abundance that have been previously identified in laboratory-based studies. Our study represents the first iRF application to marine algal blooms that helps to identify ocean, microbial, and terrestrial conditions that are considered dominant causal factors on bloom dynamics.