Utilizing a comparative approach to assess genome evolution during diploidization in Artemisia tridentata, a keystone species of western North America

PREMISE

Polyploidization is often followed by diploidization. Diploidization is generally studied using synthetic polyploid lines and/or crop plants, but rarely using extant diploids or nonmodel plants such as Artemisia tridentata. This threatened western North American keystone species has a large genome compared to congeneric Artemisia species; dominated by diploid and tetraploid cytotypes, with multiple origins of tetraploids with genome size reduction.

METHODS

The genome of an A. tridentata sample was resequenced to study genome evolution and compared to that of A. annua, a diploid congener. Three diploid genomes of A. tridentata were compared to test for multiple diploidization events.

RESULTS

The A. tridentata genome had many chromosomal rearrangements relative to that of A. annua, while large-scale synteny of A. tridentata chromosome 3 and A. annua chromosome 4 was conserved. The three A. tridentata genomes had similar sizes (4.19-4.2 Gbp), heterozygosity (2.24-2.25%), and sequence (98.73-99.15% similarity) across scaffolds, and in k-mer analyses, similar patterns of diploid heterozygous k-mers (AB = 41%, 47%, and 47%), triploid heterozygous k-mers (AAB = 18-21%), and tetraploid k-mers (AABB = 13-17%). Biallelic SNPs were evenly distributed across scaffolds for all individuals. Comparisons of transposable element (TE) content revealed differential enrichment of TE clades.

CONCLUSIONS

Our findings suggest population-level TE differentiation after a shared polyploidization-to-diploidization event(s) and exemplify the complex processes of genome evolution. This research approached provides new resources for exploration of abiotic stress response, especially the roles of TEs in response pathways.

Elevation-associated pathways mediate aquatic biodiversity at multi-trophic levels along a plateau inland river

Aquatic biodiversity plays a significant role in maintaining the ecological balance and the overall health of riverine ecosystems. Elevation is an important factor influencing biodiversity patterns. However, it is still unclear through which pathway elevation influences riverine biodiversity at different trophic levels. In this study, the elevation-associated pathways affecting aquatic biodiversity at different trophic levels were explored using structural equation modeling (SEM) and taking the Bayin River, China as the case. The results showed that the elevational patterns were different among aquatic organisms at different trophic levels. For macroinvertebrates and bacteria, the pattern was hump-shaped; while for phytoplankton and zooplankton, it was U-shaped. Building upon these observed elevational patterns, our investigation delved into the direct and indirect pathways through which elevation influences aquatic biodiversity. We found that elevation exerts an impact on aquatic biodiversity via indirect pathways. For all aquatic organisms investigated, the major pathway through which elevation influences biodiversity is mediated by water temperature and water quality. For aquatic organisms at higher trophic levels, like macroinvertebrates and zooplankton, the crucial pathway is also mediated by the landscape. The results of this study contributed to understanding the effects of elevation on aquatic organisms at different trophic levels and provided an important basis for the assessment of riverine biodiversity at large scales.

An Appraisal of Nonmicrobial Biostimulants' Impact on the Productivity and Mineral Content of Wild Rocket (Diplotaxis tenuifolia (L.) DC.) Cultivated under Organic Conditions

Modern agriculture urgently requires viable alternatives to synthetic chemical substances, such as pesticides and fertilizers, to comply with new and stringent international regulations and meet the growing demands of consumers who prefer chemical-free food. Consequently, organic agriculture has garnered increasing interest over time. To compensate for yield reduction resulting from opting out of the use mineral fertilizers, research has focused on the use of biostimulants to sustain the productivity of horticultural crops. To this end, a greenhouse experiment was conducted to assess the effects of three nonmicrobial biostimulants (a plant extract, vegetable protein hydrolysate, and a seaweed extract) and an untreated control on the production and mineral content of wild rocket (Diplotaxis tenuifolia (L.) DC.) cultivated under organic conditions and harvested three times during the growth cycle. In general, the nitrate content, which defines the commercial quality of wild rocket, was not influenced by the application of biostimulants. At each harvest, the application of biostimulants resulted in improved production performance, although this was not always accompanied by an increase in mineral content. Specifically, the best results were obtained with the use of plant-derived protein hydrolysate and plant extract, which led to an improvement in total yield of 32.1% and 27.2%, respectively compared to that of control plants. These results reconfirm that biostimulants represent a valid and indispensable tool for organic growers.

Nitrogen enrichment changed the biogeochemical role of sesarmid crabs by shifting their diets in tropical mangrove ecosystems

Sesarmid crabs modulate nutrient dynamics of tropical mangroves through their leaf-eating habit. How N enrichment may alter this regulatory role, and the implications for mangrove nutrient dynamics, remain unclear. Using a mesocosm experiment, we tested how N enrichment could change the microphytobenthos (MPB) communities, thus modifying the crabs' diet and their role in nutrient dynamics. The factorial experiment combined with field investigation revealed a significant increase in the relative abundance of cyanobacteria. Stable isotope analysis suggested that the main carbon source of crabs shifted from leaf litter to cyanobacteria in mesocosms under both high (20×) and low (2×) N enrichment treatments. The significantly lower total cellulase activity of crabs in the mesocosms might explain the decreased carbon assimilation from leaf litter. The changes in the MPB and the microbiome with N enrichment in the presence of crabs may drive significantly higher carbon processing rate in tropical mangroves.

Comparative life cycle assessment of environmental impacts and economic feasibility of tomato cultivation systems in northern plains of India

To meet the growing demand for vegetable production and promote sustainable agriculture, it is imperative to implement effective input management and adopt eco-friendly farming practices. This study aims to compare the environmental impacts of conventional and organic tomato cultivation in the northern plains of India. This study utilizes SimaPro 9.1.1 software for a comprehensive cradle-to-farm gate Life Cycle Assessment (LCA), assessing production stages, identifying key environmental factors, and incorporating ReCiPe Midpoint and Endpoint methods with one-hectare as a functional unit. Findings reveal that conventional cultivation is more affected by fertilizer application and transplanting, while organic cultivation emphasizes transplanting and irrigation. Organic cultivation contributes 904.708 kg CO2, while conventional cultivation contributes 1307.917 kg CO2 to Global Warming potential. Switching to organic cultivation leads to a significant 35.04% decrease in all impact categories. Using the endpoint method, organic cultivation achieves a notable 27.16% reduction, scoring 58.30 compared to conventional cultivation's 80.04. The LCA analysis of tomato cultivation highlights Fertilizer application as the predominant environmental concern, emphasizing the need for sustainable techniques to minimize waste and mitigate environmental impacts. This study recommends imposing restrictions on fertilizer and pesticide use and formulating effective policies to promote the adoption of sustainable practices.

Exposure assessment of plastics, phthalate plasticizers and their transformation products in diverse bio-based fertilizers

Bio-based fertilizers (BBFs) produced from organic waste have the potential to reduce societal dependence on limited and energy-intensive mineral fertilizers. BBFs, thereby, contribute to a circular economy for fertilizers. However, BBFs can contain plastic fragments and hazardous additives such as phthalate plasticizers, which could constitute a risk for agricultural soils and the environment. This study assessed the exposure associated with plastic and phthalates in BBFs from three types of organic wastes: agricultural and food industry waste (AgriFoodInduWaste), sewage sludge (SewSludge), and biowaste (i.e., garden, park, food and kitchen waste). The wastes were associated with various treatments like drying, anaerobic digestion, and vermicomposting. The number of microplastics (0.045-5 mm) increased from AgriFoodInduWaste-BBFs (15-258 particles g-1), to SewSludge-BBFs (59-1456 particles g-1) and then to Biowaste-BBFs (828-2912 particles g-1). Biowaste-BBFs mostly contained packaging plastics (e.g., polyethylene terephthalate), with the mass of plastic (>10 g kg-1) exceeding the EU threshold (3 g kg-1, plastics >2 mm). Other BBFs mostly contained small (< 1 mm) non-packaging plastics in amounts below the EU limit. The calculated numbers of microplastics entering agricultural soils via BBF application was high (107-1010 microplastics ha-1y-1), but the mass of plastic released from AgriFoodInduWaste-BBFs and SewSludge-BBFs was limited (< 1 and <7 kg ha-1y-1) compared to Biowaste-BBFs (95-156 kg ha-1y-1). The concentrations of di(2-ethylhexyl)phthalate (DEHP; < 2.5 mg kg-1) and phthalate transformation products (< 8 mg kg-1) were low (< benchmark of 50 mg kg-1 for DEHP), attributable to both the current phase-out of DEHP as well as phthalate degradation during waste treatment. The Biowaste-BBF exposed to vermicomposting indicated that worms accumulated phthalate transformation products (4 mg kg-1). These results are overall positive for the implementation of the studied AgriFoodInduWaste-BBFs and SewSludge-BBFs. However, the safe use of the studied Biowaste-BBFs requires reducing plastic use and improving sorting methods to minimize plastic contamination, in order to protect agricultural soils and reduce the environmental impact of Biowaste-BBFs.

Temperature and nutrients alter the relative importance of stochastic and deterministic processes in the coastal macroinvertebrates biodiversity assembly on long-time scales

Macroinvertebrates play a vital role in coastal ecosystems and are an important indicator of ecosystem quality. Both anthropogenic activity and environmental changes may lead to significant changes in the marine macroinvertebrate community. However, the assembly process of benthic biodiversity and its mechanism driven by environmental factors at large scales remains unclear. Here, using the benthic field survey data of 15 years at large spatial and temporal scales from the Yellow Sea Large Marine Ecosystem, we investigated the relative importance of environmental selection, dispersal processes, random-deterministic processes of macroinvertebrates community diversity assembly, and the responses of this relative importance driven by temperature and nutrients. Results showed that the macroinvertebrates community diversity is mainly affected by dispersal. Nitrogen and phosphorus are the most important negative factors among environmental variables, while geographical distance is the main limiting factor of β diversity. Within the range of 0.35-0.70 mg/L of nutrients, increasing nutrient concentration can significantly facilitate the contribution of the decay effect to β diversity. Within the temperature range studied (15.0-18.0°C), both warming and cooling can lead to a greater tendency for species diversity assembly processes to be dominated by deterministic processes. The analysis contributes to a better understanding of the assembly process of the diversity of coastal marine macroinvertebrates communities and how they adapt to global biogeochemical processes.

Mapping the ratio of agricultural inputs to yields reveals areas with potentially less sustainable farming

Fertilisers and pesticides are major sources of the environmental harm that results from farming, yet it remains difficult to target reductions in their impacts without compromising food production. We suggest that calculating the ratio of agrochemical inputs to yield can provide an indication of the potential sustainability of farmland, with those areas that have high input relative to yield being considered as less sustainable. Here we design an approach to characterise such Input to Yield Ratios (IYR) for four inputs that can be plausibly linked to environmental impacts: the cumulative risk resulting from pesticide exposure for honeybees and for earthworms, and the amount of nitrogen or phosphorus fertiliser applied per unit area. We capitalise on novel national-scale data to assess IYR for wheat farming across all of England. High-resolution spatial patterns of IYR differed among the four inputs, but hotspots, where all four IYRs were high, were in key agricultural regions not usually characterised as having low suitability for cropping. By scaling the magnitude of each input against crop yield, the IYR does not penalise areas of high yield with higher inputs (important for food production), or areas with low yields but which are achieved with low inputs (important as low impact areas). Instead, the IYR provides a globally applicable framework for evaluating the broad patterns of trade-offs between production and environmental risk, as an indicator of the potential for harm, over large scales. Its use can thus inform targeting to improve agricultural sustainability, or where one might switch to other land uses such as ecosystem restoration.

Airport Deicers: An Unrecognized Source of Phosphorus Loading in Receiving Waters

Airport ice control products contributed to total phosphorus (TP) loadings in a study of surface water runoff at a medium-sized airport from 2015 to 2021. Eleven airport ice control products had TP concentrations from 1-807 mg L-1 in liquid formulas, while solid pavement deicer had a TP concentration of 805 mg kg-1. Product application data, formula TP concentrations, and surface water sampling results were used to estimate TP concentration and loading contributions from these ice control products to receiving streams. Airport ice control products were found to contribute to TP in 84% of the water samples collected at downstream sites during deicing events, and TP concentrations at those sites exceeded aquatic life benchmarks in 70% of samples collected during deicing. A receiving stream 6 km downstream had TP attributed to airport ice control sources in 78% of the samples. TP loadings at an upstream site and the receiving stream site were greatest during the largest runoff events as is typical in urban runoff, but this pattern was not always followed at airport outfall sites due to the influence of TP in deicer products. Products analyzed in this study are used at airports across the United States and abroad, and findings suggest that airport deicers could represent a previously unrecognized source of phosphorus to adjacent waterways.

Integrating genome-wide association study with transcriptomic data to predict candidate genes influencing Brassica napus root and biomass-related traits under low phosphorus conditions

BACKGROUND

Rapeseed (Brassica napus L.) is an essential source of edible oil and livestock feed, as well as a promising source of biofuel. Breeding crops with an ideal root system architecture (RSA) for high phosphorus use efficiency (PUE) is an effective way to reduce the use of phosphate fertilizers. However, the genetic mechanisms that underpin PUE in rapeseed remain elusive. To address this, we conducted a genome-wide association study (GWAS) in 327 rapeseed accessions to elucidate the genetic variability of 13 root and biomass traits under low phosphorus (LP; 0.01 mM P +). Furthermore, RNA-sequencing was performed in root among high/low phosphorus efficient groups (HP1/LP1) and high/low phosphorus stress tolerance groups (HP2/LP2) at two-time points under control and P-stress conditions.

RESULTS

Significant variations were observed in all measured traits, with heritabilities ranging from 0.47 to 0.72, and significant correlations were found between most of the traits. There were 39 significant trait-SNP associations and 31 suggestive associations, which integrated into 11 valid quantitative trait loci (QTL) clusters, explaining 4.24-24.43% of the phenotypic variance observed. In total, RNA-seq identified 692, 1076, 648, and 934 differentially expressed genes (DEGs) specific to HP1/LP1 and HP2/LP2 under P-stress and control conditions, respectively, while 761 and 860 DEGs common for HP1/LP1 and HP2/LP2 under both conditions. An integrated approach of GWAS, weighted co-expression network, and differential expression analysis identified 12 genes associated with root growth and development under LP stress. In this study, six genes (BnaA04g23490D, BnaA09g08440D, BnaA09g04320D, BnaA09g04350D, BnaA09g04930D, BnaA09g09290D) that showed differential expression were identified as promising candidate genes for the target traits.

CONCLUSION

11 QTL clusters and 12 candidate genes associated with root and development under LP stress were identified in this study. Our study's phenotypic and genetic information may be exploited for genetic improvement of root traits to increase PUE in rapeseed.

Recurrent allopolyploidizations diversify ecophysiological traits in marsh orchids (Dactylorhiza majalis s.l.)

Whole-genome duplication has shaped the evolution of angiosperms and other organisms, and is important for many crops. Structural reorganization of chromosomes and repatterning of gene expression are frequently observed in allopolyploids, with physiological and ecological consequences. Recurrent origins from different parental populations are widespread among polyploids, resulting in an array of lineages that provide excellent models to uncover mechanisms of adaptation to divergent environments in early phases of polyploid evolution. We integrate here transcriptomic and ecophysiological comparative studies to show that sibling allopolyploid marsh orchid species (Dactylorhiza, Orchidaceae) occur in different habitats (low nutrient fens vs. meadows with mesic soils) and are characterized by a complex suite of intertwined, pronounced ecophysiological differences between them. We uncover distinct features in leaf elemental chemistry, light-harvesting, photoprotection, nutrient transport and stomata activity of the two sibling allopolyploids, which appear to match their specific ecologies, in particular soil chemistry differences at their native sites. We argue that the phenotypic divergence between the sibling allopolyploids has a clear genetic basis, generating ecological barriers that maintain distinct, independent lineages, despite pervasive interspecific gene flow. This suggests that recurrent origins of polyploids bring about a long-term potential to trigger and maintain functional and ecological diversity in marsh orchids and other groups.

Samad MY, Ramlan MF, Mokhatar SJ. Short-Term Effects of Bokashi Fertilizer with Reduced NPK Fertilization on Soil Fertility, Growth, and Yield of Rubber Trees

Rubber is currently the second major industrial crop in Malaysia after oil palm. The use of bokashi fertilizer (BF) on industrial crops is still not popular, and farmers rely mostly on chemical fertilizers (CFs) that are costly and hazardous to the environment. This research was conducted at Hevea plantation, Universiti Putra Malaysia, between August 2020–October 2021. The study was to assess the short-term effects of BF with reduced NPK fertilization on soil fertility, growth, and yield of rubber. Seven treatments (T) were involved. T1, T2, and T3 denote 4, 8, and 12 kg BF per pit. T4 was 1 kg NPK as control, whereas T5, T6, and T7 denote 4, 8, and 12 kg BF + 500 g NPK per pit, respectively. The variables observed included total nitrogen (TN%), total phosphorus (TP%), organic carbon (OC%), organic matter (OM%), exchangeable cations, microbial counts, tree girth, and dry rubber yield. The major findings indicated that applying 12 kg BF has raised the soil’s TN%, OC%, and OM% by 165, 171.4, and 172.0%, respectively, compared to NPK control. Also, adding 4 kg BF + 500 g NPK has increased the soil’s cation exchange capacity and TP% values by 107.8 and 42.9%, respectively, compared to the control. Adding sole bokashi increased the bacterial population by 22.2–133.3%. Rubber yield was better on trees treated with 12 kg BF, though this did not differ significantly from other treatments. Therefore, applying 12 kg BF or 4 kg BF + 500 g NPK can improve soil fertility and save costs from using inorganic fertilizer by at least 50%.

Polyploidy impacts population growth and competition with diploids: multigenerational experiments reveal key life-history trade-offs

Ecological theory predicts that early generation polyploids ('neopolyploids') should quickly go extinct owing to the disadvantages of rarity and competition with their diploid progenitors. However, polyploids persist in natural habitats globally. This paradox has been addressed theoretically by recognizing that reproductive assurance of neopolyploids and niche differentiation can promote establishment. Despite this, the direct effects of polyploidy at the population level remain largely untested despite establishment being an intrinsically population-level process. We conducted population-level experiments where life-history investment in current and future growth was tracked in four lineage pairs of diploids and synthetic autotetraploids of the aquatic plant Spirodela polyrhiza. Population growth was evaluated with and without competition between diploids and neopolyploids across a range of nutrient treatments. Although neopolyploid populations produce more biomass, they reach lower population sizes and have reduced carrying capacities when growing alone or in competition across all nutrient treatments. Thus, contrary to individual-level studies, our population-level data suggest that neopolyploids are competitively inferior to diploids. Conversely, neopolyploid populations have greater investment in dormant propagule production than diploids. Our results show that neopolyploid populations should not persist based on current growth dynamics, but high potential future growth may allow polyploids to establish in subsequent seasons.

Large-scale prediction of stream water quality using an interpretable deep learning approach

Deep learning methods, which have strong capabilities for mapping highly nonlinear relationships with acceptable calculation speed, have been increasingly applied for water quality prediction in recent studies. However, it is argued that the practicality of deep learning methods is limited due to the lack of physical mechanics to explain the prediction results of water quality changes. A knowledge gap exists in rationalizing the deep learning results for water quality predictions. To address this gap, an interpretable deep learning framework was established to predict the spatiotemporal variations of water quality parameters in a large spatial region. Mereological, land-use, and socioeconomic variables were adopted to predict the daily variations of stream water quality parameters across 138 sub-catchments in a total of over 575,250 km² in southern China. The coefficients of determination of chemical oxygen demand (COD), total phosphorus (TP), and total nitrogen (TN) predictions were over 0.80, suggesting a satisfactory prediction performance. The model performance in terms of prediction accuracy could be improved by involving land-use and socioeconomic predictors in addition to hydrological variables. The SHapley Additive exPlanations method used in this study was demonstrated to be effective for interpreting the prediction results by identifying the significant variables and reasoning their influencing directions on the variation of each water quality parameter. The air temperature, proportion of forest area, grain production, population density, and proportion of urban area in each sub-catchment as well as the accumulated rainfall within the previous 3 days were identified as the most significant variables affecting the variations of dissolved oxygen, COD, ammoniacal nitrogen(NH₃-N), TN, TP, and turbidity in the stream water in the case area, respectively.

Phytoremediation of nitrogen and phosphorus pollutants from glass industry effluent by using water hyacinth (Eichhornia crassipes (Mart.) Solms): Application of RSM and ANN techniques for experimental optimization

The present study aimed to assess the efficiency of the water hyacinth (Eichhornia crassipes (Mart.) Solms) plant for the reduction of nitrogen and phosphorus pollutants from glass industry effluent (GIE) as batch mode phytoremediation experiments. For this, response surface methodology (RSM) and artificial neural networks (ANN) methods were adopted to evidence the optimization and prediction performances of E. crassipes for total Kjeldahl's nitrogen (TKN) and total phosphorus (TP) removal. The control parameters, i.e., GIE concentration (0, 50, and 100%) and plant density (1, 3, and 5 numbers) were used to optimize the best reduction conditions of TKN and TP. A quadratic model of RSM and feed-forward backpropagation algorithm-based logistic model (input layer: 2 neurons, hidden layer: 10 neurons, and output layer: 1 neuron) of ANN showed good fitness results for experimental optimization. Optimization results showed that maximum reduction of TKN (93.86%) and TP (87.43%) was achieved by using 60% of GIE concentration and nearly five plants. However, coefficient of determination (R²) values showed that ANN models (TKN: 0.9980; TP: 0.9899) were superior in terms of prediction performance as compared to RSM (TKN: 0.9888; TP: 0.9868). Therefore, the findings of this study concluded that E. crassipes can be effectively used to remediate nitrogen and phosphorus loads of GIE and minimize environmental hazards caused by its unsafe disposal.

Experiments are needed to quantify the main causes of insect decline

Sparked by reports of insect declines of unexpected extent, there has been a surge in the compilation and analysis of insect time series data. While this effort has led to valuable databases, disagreement remains as to whether, where and why insects are declining. The 'why' question is particularly important because successful insect conservation will need to address the most important drivers of decline. Despite repeated calls for more long-term data, new time series will have to run for decades to quantitatively surpass those currently available. Here we argue that experimentation in addition to quantitative analysis of existing data is needed to identify the most important drivers of insect decline. While most potential drivers of insect population change are likely to have already been identified, their relative importance is largely unknown. Researchers should thus unite and use statistical insight to set up suitable experiments to be able to rank drivers by their importance. Such a coordinated effort is needed to produce the knowledge necessary for conservation action and will also result in increased monitoring and new time series.

Plant-growth promotion by proteobacterial strains depends on the availability of phosphorus and iron in Arabidopsis thaliana plants

Phosphorus (as phosphate, Pi) and iron (Fe) are critical nutrients in plants that are often poorly available in the soil and can be microbially affected. This work aimed to evaluate how plant-rhizobacteria interaction changes due to different Pi or Fe nutritional scenarios and to study the underlying molecular mechanisms of the microbial modulation of these nutrients in plants. Thus, three proteobacteria (Paraburkholderia phytofirmans PsJN, Azospirillum brasilense Sp7, and Pseudomonas putida KT2440) were used to inoculate Arabidopsis seeds. Additionally, the seeds were exposed to a nutritional factor with the following levels for each nutrient: sufficient (control) or low concentrations of a highly soluble source or sufficient concentrations of a low solubility source. Then, the effects of the combinatorial factors were assessed in plant growth, nutrition, and genetic regulation. Interestingly, some bacterial effects in plants depended on the nutrient source (e.g., increased aerial zones induced by the strains), and others (e.g., decreased primary roots induced by Sp7 or KT2440) occurred regardless of the nutritional treatment. In the short-term, PsJN had detrimental effects on plant growth in the presence of the low-solubility Fe compound, but this was not observed in later stages of plant development. A thorough regulation of the phosphorus content was detected in plants independent of the nutritional treatment. Nevertheless, inoculation with KT2440 increased P content by 29% Pi-deficiency exposed plants. Conversely, the inoculation tended to decrease the Fe content in plants, suggesting a competition for this nutrient in the rhizosphere. The P-source also affected the effects of the PsJN strain in a double mutant of the phosphate starvation response (PSR). Furthermore, depending on the nutrient source, PsJN and Sp7 strains differentially regulated PSR and IAA- associated genes, indicating a role of these pathways in the observed differential phenotypical responses. In the case of iron, PsJN and SP7 regulated iron uptake-related genes regardless of the iron source, which may explain the lower Fe content in inoculated plants. Overall, the plant responses to these proteobacteria were not only influenced by the nutrient concentrations but also by their availabilities, the elapsed time of the interaction, and the specific identities of the beneficial bacteria. Graphical AbstractThe effects of the different nutritional and inoculation treatments are indicated for plant growth parameters (A), gene regulation (B) and phosphorus and iron content (C). Figures created with BioRender.com with an academic license.

Strategies for Restoring and Managing Ecological Corridors of Freshwater Ecosystem

Along with accelerating urbanization and associated anthropogenic disturbance, the structure and function of freshwater ecosystems worldwide are substantially damaged. To improve ecosystem health, and thus enhance the ecosystem security of the urban ecosystem, numbers of management approaches and engineering projects have been applied to mitigate the degradation of freshwaters. Nevertheless, there is still a lack of comprehensive and systematic research on the ecological corridor restoration of freshwater ecosystems; especially for Suzhou Grand Canal, one section of the world's longest and ancient Grand Canal which is inclined to severe ecosystem degradation. Through investigating the adjacent land use characteristics, habitat quality, vegetation cover, instream water quality, and habitat composition, we aimed to: (i) assess the water quality of the Suzhou Grand Canal; (ii) evaluate the ecological characteristics of the canal ecosystem; (iii) develop strategic countermeasures to restore the ecological corridors for the mitigation of ecological problems. The results demonstrated: a large built area, a smaller ecological zone, a low habitat quality and habitat connectivity, and a high degree of habitat fragmentation within the canal corridor, also a simplified instream habitat composition, and greater nutrient and COD concentrations in the surface water-especially in the upstream and midstream canal. All urbanization-induced multiple stressors, such as land use changes, altered hydrology, and the simplified riparian zone et al., contributed synergistically to the degradation of the canal ecosystem. To alleviate the ecosystem deterioration, three aspects of recommendations were proposed: water pollution control, watershed ecosystem restoration, and ecological network construction. Basically, building a comprehensive watershed ecological network-on the basis of associated ecosystem restoration, and the connection of multi-dimensional ecological corridors-would dramatically increase the maintenance of aquatic-terrestrial system biodiversity, and improve the regional ecological security pattern and watershed resilience toward stochastic future disturbances. This study contributes to the understanding of the ecological challenges and related causes of the canal ecosystem. The integrated strategy introduced in this study provides policymakers, water resource managers, and planners with comprehensive guidelines to restore and manage the ecological corridor of the canal ecosystem. This can be used as a reference in freshwater ecosystems elsewhere, to improve ecosystem stability for supporting the sustainable development of urban ecosystems.

Phosphorus Recycling, Biocontrol, and Growth Promotion Capabilities of Soil Bacterial Isolates from Mexican Oak Forests: An Alternative to Reduce the Use of Agrochemicals in Maize Cultivation

Six bacteria (Bacillus velezensis 13, Bacillus subtillis 42, Pseudomonas fluorescens E221, Pseudomonas Poae EE12, Rahnella sp. EM1, and Serratia sp. EM2) isolated from the soil and litter of Mexican oak forests were characterized by identifying their ability to acquire phosphorus from different sources, analyzed for their biocontrol capabilities against two different phytopathogenic fungi, and finally tested for their ability to stimulate the germination of maize seeds and promotion of maize seedling growth. The greatest capacity to biocontrol the mycelial growth of phytopathogenic fungi Botrytis cinerea and Fusarium oxysporum was found in B. velezensis 13 and B. subtillis 42. P. poae EE12 and P. fluorescens E221 significantly promoted germination and the length of the primary root in Zea mays. Rahnella sp. EM1 and Serratia sp. EM2 could produce indole compounds related to auxin synthesis and increased the fresh weight of the maize seedlings. Together, these isolates represent an alternative to reduce the use of agrochemicals in maize cultivation. In general, soil microorganisms from Mexican oak forests represent a source of genetic resources for the sustainable management and conservation of soils for agricultural use.

Nonlinear effects of environmental drivers shape macroinvertebrate biodiversity in an agricultural pondscape

Agriculture is a leading cause of biodiversity loss and significantly impacts freshwater biodiversity through many stressors acting locally and on the landscape scale. The individual effects of these numerous stressors are often difficult to disentangle and quantify, as they might have nonlinear impacts on biodiversity. Within agroecosystems, ponds are biodiversity hotspots providing habitat for many freshwater species and resting or feeding places for terrestrial organisms. Ponds are strongly influenced by their terrestrial surroundings, and understanding the determinants of biodiversity in agricultural landscapes remains difficult but crucial for improving conservation policies and actions. We aimed to identify the main effects of environmental and spatial variables on α‐, β‐, and γ‐diversities of macroinvertebrate communities inhabiting ponds (n = 42) in an agricultural landscape in the Northeast Germany, and to quantify the respective roles of taxonomic turnover and nestedness in the pondscape. We disentangled the nonlinear effects of a wide range of environmental and spatial variables on macroinvertebrate α‐ and β‐biodiversity. Our results show that α‐diversity is impaired by eutrophication (phosphate and nitrogen) and that overshaded ponds support impoverished macroinvertebrate biota. The share of arable land in the ponds' surroundings decreases β‐diversity (i.e., dissimilarity in community), while β‐diversity is higher in shallower ponds. Moreover, we found that β‐diversity is mainly driven by taxonomic turnover and that ponds embedded in arable fields support local and regional diversity. Our findings highlight the importance of such ponds for supporting biodiversity, identify the main stressors related to human activities (eutrophication), and emphasize the need for a large number of ponds in the landscape to conserve biodiversity. Small freshwater systems in agricultural landscapes challenge us to compromise between human demands and nature conservation worldwide. Identifying and quantifying the effects of environmental variables on biodiversity inhabiting those ecosystems can help address threats impacting freshwater life with more effective management of pondscapes.

Water and nutrient availability exert selection on reproductive phenology

PREMISE

Global change has changed resource availability to plants, which could shift the adaptive landscape. We hypothesize that novel water and nutrient availability combinations alter patterns of natural selection on reproductive phenology in Boechera stricta (Brassicaceae) and influence the evolution of local adaptation.

METHODS

We conducted a multifactorial greenhouse study using 35 accessions of B. stricta sourced from a broad elevational gradient in the Rocky Mountains. We exposed full siblings to three soil water and two nutrient availability treatment levels, reflecting current and projected future conditions. In addition, we quantified fitness (seed count) and four phenological traits: the timing of first flowering, the duration of flowering, and height and leaf number at flowering.

RESULTS

Selection favored early flowering and longer duration of flowering, and the genetic correlation between these traits accorded with the direction of selection. In most treatments, we found selection for increased height, but selection on leaf number depended on water availability, with selection favoring more leaves in well-watered conditions and fewer leaves under severe drought. Low-elevation genotypes had the greatest fitness under drought stress, consistent with local adaptation.

CONCLUSIONS

We found evidence of strong selection on these heritable traits. Furthermore, the direction and strength of selection on size at flowering depended on the variable measured (height vs. leaf number). Finally, selection often favored both early flowering and a longer duration of flowering. Selection on these two components of phenology can be difficult to disentangle due to tight genetic correlations.

Mining synergistic genes for nutrient utilization and disease resistance in maize based on co-expression network and consensus QTLs

Nutrient restrictions and large-scale emergence of diseases are threatening the maize production. Recent findings demonstrated that there is a certain synergistic interaction between nutrition and diseases pathways in model plants, however there are few studies on the synergistic genes of nutrients and diseases in maize. Thus, the transcriptome data of nitrogen (N) and phosphorus (P) nutrients and diseases treatments in maize, rice, wheat and Arabidopsis thaliana were collected in this study, and four and 22 weighted co-expression modules were obtained by using Weighted Gene Co-expression Network Analysis (WGCNA) in leaf and root tissues, respectively. With a total of 5252 genes, MFUZZ cluster analysis screened 26 clusters with the same expression trend under nutrition and disease treatments. In the meantime, 1427 genes and 22 specific consensus quantitative trait loci (scQTLs) loci were identified by meta-QTL analysis of nitrogen and phosphorus nutrition and disease stress in maize. Combined with the results of cluster analysis and scQTLs, a total of 195 consistent genes were screened, of which six genes were shown to synergistically respond to nutrition and disease both in roots and leaves. Moreover, the six candidate genes were found in scQTLs associated with gray leaf spot (GLS) and corn leaf blight (CLB). In addition, subcellular localization and bioinformatics analysis of the six candidate genes revealed that they were primarily expressed in endoplasmic reticulum, mitochondria, nucleus and plasma membrane, and were involved in defense and stress, MeJA and abscisic acid response pathways. The fluorescence quantitative PCR confirmed their responsiveness to nitrogen and phosphorus nutrition as well as GLS treatments. Taken together, findings of this study indicated that the nutrition and disease have a significant synergistic response in maize.

Nitrogen loadings affect trophic structure in stream food webs on the Tibetan Plateau, China

Anthropogenic activities, such as agricultural and industrial development, have increased nutrient inputs into waterways, which affect trophic interactions and the flow of energy through food webs in the aquatic ecosystems. However, the responses of food web structure and function to specific anthropogenic stressors in the alpine stream systems remain unclear. Here, we studied the stream food webs in the Lhasa River on the Tibetan Plateau, China. We measured the isotopic ratios (δ¹³C and δ¹⁵N) of macroinvertebrate and fish functional feeding groups (FFGs) and their basal resources in the streams. Dietary contributions of basal resources to consumers and food web metrics including trophic length, diversity, and redundancy were used to quantify changes in stream food webs in response to anthropogenic disturbance. Dietary analysis showed that allochthonous resources contributed more than autochthonous resources to macroinvertebrate primary consumers regardless of the disturbance intensity in the adjacent land areas. Anthropogenic activities increased the δ¹⁵N values in epilithic algae and isotopic variation in basal resources and fish but reduced the trophic length and redundancy (i.e., fewer species or taxon at each trophic level) in food webs. Additionally, the total nitrogen concentration in waters was the most important environmental variable affecting trophic diversity and redundancy. Therefore, the reduction of nitrogen inputs into streams is critical for sustainable river management and biodiversity conservation in the streams on the Tibetan Plateau.

The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat 'communities' are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat 'community' composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat 'communities'.

Do water and soil nutrient scarcities differentially impact the performance of diploid and tetraploid Solidago gigantea (Giant Goldenrod, Asteraceae)?

Plants require water and nutrients for survival, although the effects of their availabilities on plant fitness differ amongst species. Genome size variation, within and across species, is suspected to influence plant water and nutrient requirements, but little is known about how variations in these resources concurrently affect plant fitness based on genome size. We examined how genome size variation between autopolyploid cytotypes influences plant morphological and physiological traits, and whether cytotype-specific trait responses differ based on water and/or nutrient availability. Diploid and autotetraploid Solidago gigantea (Giant Goldenrod) were grown in a greenhouse under four soil water:N+P treatments (L:L, L:H, H:L, H:H), and stomata characteristics (size, density), growth (above- and belowground biomass, R/S), and physiological (A_net , E, WUE) responses were measured. Resource availabilities and cytotype identity influenced some plant responses but their effects were independent of each other. Plants grown in high-water and nutrient treatments were larger, plants grown in low-water or high-nutrient treatments had higher WUE but lower E, and A_net and E rates decreased as plants aged. Autotetraploids also had larger and fewer stomata, higher biomass and larger A_net than diploids. Nutrient and water availability could influence intra- and interspecific competitive outcomes. Although S. gigantea cytotypes were not differentially affected by resource treatments, genome size may influence cytogeographic range patterning and population establishment likelihood. For instance, the larger size of autotetraploid S. gigantea might render them more competitive for resources and niche space than diploids.

Stoichiometry versus ecology: the relationships between genome size and guanine-cytosine content, and tissue nitrogen and phosphorus in grassland herbs

BACKGROUND AND AIMS

Plant tissue nitrogen (N) and phosphorus (P) and genome traits, such as genome size and guanine-cytosine (GC) content, scale with growth or metabolic rates and are linked to plant ecological strategy spectra. Tissue NP stoichiometry and genome traits are reported to affect plant growth, metabolic rates or ecological strategies in contrasting ways, although the elemental costs for building and maintaining DNA are typically overlooked.

METHODS

We formulated stoichiometry- and ecology-based predictions on the relationship between genome size and GC content to tissue N, P and N : P and tested them on a set of 130 herbaceous species from a temperate grassland using ordinary, phylogenetic and quantile regression.

KEY RESULTS

Genome size was only negatively linked to plant N and N : P in species with very small genomes. We found no link between genome size and plant P. GC content was negatively linked to plant N and P but we found these significant links consistently in both GC-rich and GC-poor species. Finally, GC content correlated positively with plant N : P but only in species with GC-rich genomes.

CONCLUSIONS

Our results provide stronger support for the ecology-based predictions than the stoichiometry-based predictions, and for the links between GC content and plant N and P stoichiometry than for genome size. We argue that the theories of plant metabolic rates and ecological strategies (resource-acquisitive vs. conservative or ruderal vs. stress-tolerator spectra) better explain interspecific genome-NP stoichiometry relationships at the tissue level (although relatively weakly) than the stoichiometric theory based on the elemental costs for building and maintaining DNA.

Spotted knapweed (Centaurea stoebe) creates a soil legacy effect by modulating soil elemental composition in a semi-arid grassland ecosystem

Invasive plants such as spotted knapweed (Centaurea stoebe) are particularly detrimental to fragile ecosystems like semi-arid grasslands in the interior British Columbia, impacting aboveground and belowground ecology. Physical removal of C. stoebe has been one of the most popular invasive species management strategies, but the impact of C. stoebe removal on soil has hardly been studied. Here, we examine the legacy effect of C. stoebe on soil elemental composition and ecosystem function following its removal in the Lac Du Bios Grasslands Protected Area, British Columbia. First, we selected 40 paired C. stoebe invaded and control (uninvaded) plots and removed all vegetation from these plots. We planted Festuca campestris seedlings in these plots and harvested and weighed the biomass after four months. Additionally, we quantified total carbon and nitrogen in soil. We observed that C. stoebe invaded plots had significantly lower F. campestris biomass. Moreover, the total carbon and nitrogen content, and carbon/nitrogen ratio were significantly lower in C. stoebe invaded plots. We further analyzed 12 common soil elements and found the elemental composition was significantly different in C. stoebe invaded plots compared to controls. We investigated the impact of elemental composition on soil ecosystem functions (such as total soil carbon, total soil nitrogen, and F. campestris productivity). Our analysis revealed significant relationships amongst the elemental composition and total soil carbon and nitrogen, and F. campestris productivity. The results indicate that C. stoebe exerts a legacy effect by altering the soil elemental composition that may subsequently impacts soil ecosystem functions such as plant productivity and total carbon and nitrogen content.

Muddy (silty-sand) beaches in semi-arid regions attenuate the contaminants flowing into the sea as a submarine groundwater discharge

Urbanized coastal areas are well-recognized hotspots for the contaminant-enriched groundwater discharge, influencing sensitive coastal ecosystems. The present study investigates how muddy beaches in the semi-arid region alter the contaminant flux flowing into the sea using submarine groundwater discharge (SGD) estimation and hydrogeochemical analysis of coastal waters (groundwater, porewater, and seawater). Fresh SGD carries contaminants such as nutrients and trace metals in the coastal ecosystem, causing increased vulnerability towards eutrophication, harmful algal blooms, and human health. We found that SGD reaching the coast carries immense nutrient flux (155.6 mmol NO₃^- · day^-1; 35 mmol P · day^-1 and 12.4 mmol DSi · day^-1) and trace metal load ranging from 0.1 to 14.9 mmol · day^-1. The nutrient fluxes were higher in the upper saline plume compared to the lower plume. The muddy beach attenuates the nutrients in varying percentages of 9.7 to 22% of NO₃^-, 1.9 to 25.5% of P due to denitrification and phosphorus absorption, and also caused 19.6% reduction of SO₄^2-. The reduction in SO₄^2- leads to the formation of sulfide (HS^-) that promotes the metal precipitation, resulting in the removal of Pb and Cu. This attenuation of nutrients leads to a change in the nutrient ratio (N/P = 7-11) approaching the Redfield ratio, implying the vulnerability of algal bloom at the Dehri beach. Overall, the muddy beach can serve as a natural biogeochemical reactor as it attenuates the nutrient and serves as a source for certain trace metals (Fe, Mn, Zn, and Ni), altering the composition of SGD. Probably this is the first study that emphasizes the attenuation of trace metals in the muddy beaches of a semi-arid region.

Modeling Global Carbon Costs of Plant Nitrogen and Phosphorus Acquisition

Most Earth system models (ESMs) do not explicitly represent the carbon (C) costs of plant nutrient acquisition, which leads to uncertainty in predictions of the current and future constraints to the land C sink. We integrate a plant productivity-optimizing nitrogen (N) and phosphorus (P) acquisition model (fixation & uptake of nutrients, FUN) into the energy exascale Earth system (E3SM) land model (ELM). Global plant N and P uptake are dynamically simulated by ELM-FUN based on the C costs of nutrient acquisition from mycorrhizae, direct root uptake, retranslocation from senescing leaves, and biological N fixation. We benchmarked ELM-FUN with three classes of products: ILAMB, a remotely sensed nutrient limitation product, and CMIP6 models; we found significant improvements in C cycle variables, although the lack of more observed nutrient data prevents a comprehensive level of benchmarking. Overall, we found N and P co-limitation for 80% of land area, with the remaining 20% being either predominantly N or P limited. Globally, the new model predicts that plants invested 4.1 Pg C yr-1 to acquire 841.8 Tg N yr-1 and 48.1 Tg P yr-1 (1994-2005), leading to significant downregulation of global net primary production (NPP). Global NPP is reduced by 20% with C costs of N and 50% with C costs of NP. Modeled and observed nutrient limitation agreement increases when N and P are considered together (r 2 from 0.73 to 0.83).

Envisioning the manureshed: Toward comprehensive integration of modern crop and animal production

The specialization and intensification of agriculture have produced incredible gains in productivity, quality, and availability of agricultural commodities but have resulted in the separation of crop and animal production. A by-product of this separation has been the accumulation of manure regions where animal production is concentrated. Enter the "manureshed," an organizing framework for integrating animal and crop production where budgeting of manure nutrients is used to strategically guide their recycling and reuse in agricultural production systems where manure resources are of highest value. To move beyond regional nutrient balance analyses into the transformational realm required to mitigate "wicked" manure problems, manureshed management requires recognition of the challenges to systematically reorganizing resource flows. In better integrating crop and livestock systems, manureshed management must account for the unique nature of managing manure nutrients within individual livestock industries, anticipate trade-offs in substituting manure for commercial fertilizer, promote technologies to refine manure, and engage extensive social networks across scales that range from the farmgate to nation and beyond.

Dynamics and growth rate implications of ribosomes and mRNAs interaction in E. coli

Understanding how cells grow and adapt under various nutrient conditions is pivotal in the study of biological stoichiometry. Recent studies provide empirical evidence that cells use multiple strategies to maintain an optimal protein production rate under different nutrient conditions. Mathematical models can provide a solid theoretical foundation that can explain experimental observations and generate testable hypotheses to further our understanding of the growth process. In this study, we generalize a modeling framework that centers on the translation process and study its asymptotic behaviors to validate algebraic manipulations involving the steady states. Using experimental results on the growth of E. coli under C-, N-, and P-limited environments, we simulate the expected quantitative measurements to show the feasibility of using the model to explain empirical evidence. Our results support the findings that cells employ multiple strategies to maintain a similar protein production rate across different nutrient limitations. Moreover, we find that the previous study underestimates the significance of certain biological rates, such as the binding rate of ribosomes to mRNA and the transition rate between different ribosomal stages. Furthermore, our simulation shows that the strategies used by cells under C- and P-limitations result in a faster overall growth dynamics than under N-limitation. In conclusion, the general modeling framework provides a valuable platform to study cell growth under different nutrient supply conditions, which also allows straightforward extensions to the coupling of transcription, translation, and energetics to deepen our understanding of the growth process.

Heterogeneity of Spatial-Temporal Distribution of Nitrogen in the Karst Rocky Desertification Soils and Its Implications for Ecosystem Service Support of the Desertification Control—A Literature Review

In recent years, the study of soil nitrogen distribution (SND) in rocky desertification control ecosystems has increased exponentially. Rocky desertification experiences severe environmental degradation due to its fragile nature, and understanding rocky desertification soil nitrogen (SN) is critical for ecosystem services (ES) to support sustainable development. From the perspective of bibliometrics, this paper systematically, comprehensively, qualitatively and quantitatively describes the progress, trends and hotspots of SND in the field of rocky desertification environment. The results show that: 97.40% of the document type is “Article”; the study of rocky desertification SND shows the characteristics of rapid growth, the volume of published articles in the past three years accounted for 34.30% of the total; active countries are mainly China, Germany, United States, Sweden, Finland, etc. The research hotspots in this field include karst and nitrogen, and the future research hotspots tend to focus on karst rocky desertification ecosystem, soil nutrients and vegetation diversity in south China. It is suggested to construct SN management strategy suitable for rocky desertification fragile ecosystems in the future, strengthen theoretical research and comprehensively understand the characteristics of rocky desertification control ecosystem to put forward sustainable management strategy according to local conditions.

Electrochemical Sensors for Sustainable Precision Agriculture—A Review

Greenhouse gases released by agriculture account for 19% of global greenhouse gas emission. Moreover, the abuse of pesticides and fertilizers is a fundamental cause of soil and water pollution. Finding sustainable countermeasures for these problems requires completely new approaches and the integration of knowledge. Precision agriculture (PA) is a technology that reduces environmental pollution with minimal input (e.g., fertilizer, herbicides, and pesticides) and maximize the production of high-quality crops by monitoring the conditions and environment of farmland and crops. However, the lack of data—a key technology for realizing PA—remains a major obstacle to the large-scale adoption of PA. Herein, we discuss important research issues, such as data managements and analysis for accurate decision-making, and specific data acquisition strategies. Moreover, we systematically review and discuss electrochemical sensors, including sensors that monitor the plant, soil, and environmental conditions that directly affect plant growth.

Stainless steel electrochemical capacitive microneedle sensors for multiplexed simultaneous measurement of pH, nitrates, and phosphates

Concerns for agri-food safety and environmental management require development of simple to use and cost- and time-effective multiplex sensors for point-of-need (PON) chemical analytics by public end-user. Simultaneous detection of nitrates, phosphates, and pH is of importance in soil and water analysis, agriculture, and food quality assessment. This article demonstrates a suite of stainless steel microneedle electrochemical sensors for multiplexed measurement of pH, nitrate, and phosphate using faradaic capacitance derived from cyclic voltammetry as the mode of detection. The multi-target microneedle sensors were fabricated by layer-by-layer (LbL) assembly in a stainless steel hypodermic microneedle substrate. For nitrate sensing, the stainless steel was coated with carbon nanotube/cellulose nanocrystal (CNT)/CNC) decorated with silver nanoparticles (Ag). For pH measurement, the polyaniline (pANI) was coated onto the CNT/CNC@Ag film, while for phosphate detection, the CNT/CNC/Ag @pANI microneedle was further decorated with ammonium molybdenum tetrahydrate (AMT). The microelectrode platforms were characterized by FTIR, Raman, and microscopic techniques. The nitrate- and phosphate-based microneedle electrochemical sensors had excellent selectivity and sensitivity, with a determined limit of detection (LOD) of 0.008 mM and 0.007 mM, respectively. The pH microneedle sensor was responsive to pH in the linear range of 3-10. The three microneedle sensors yielded repeatable results, with a precision ranging from 4.0 to 7.5% RSD over the concentration ranges tested. The inexpensive (~ 1 $ CAD) microneedle sensors were successfully verified for use in quantification of nitrate, pH, and phosphate in brewed black coffee as a real sample. As such, the microneedle sensors are economical devices and show great promise as robust platforms for PON precision chemical analytics.

Long-Term Maternal Fertilizer Addition Increased Seed Size but Decreased Germination Capacity and Offspring Performance in Taxus baccata L

Plant fitness and species persistence depend on seed quantity and their ability to germinate and produce viable offspring. Although maternal environment can have a great impact on seed quality, few studies are pointing to the transgenerational effect of maternal environment on germination rate and offspring traits. Moreover, global changes connected to nitrogen and phosphorus deposition can also impact plants’ reproductive performance. Here, we collected Taxus baccata L. seeds produced by the same genotype female plants grown in different nutritional regimes. We use them to analyze seed size and the impact of long-term fertilization on germination capacity and offspring traits. Our results show that long-term maternal fertilizer addition increases the ratio of large seeds produced, but at the same time decreases germination capacity compared to control and nonfertilized plants. Moreover, it was demonstrated that maternal environment impacts seed traits and germination rate, and seed mass rather than maternal environment impacts offspring performance. Therefore, the study provides information on how the maternal environment regulates seed traits and germination capacity as well as seedling growth to adapt to increased nitrogen and phosphorus deposition and improves prediction about plants’ response to global environmental changes.

Geochemical Behavior of Sedimentary Phosphorus Species in Northernmost Artificial Mangroves in China

Mangroves are typically found in tropical coastal areas, and these ecosystems face deterioration and loss due to threats from climate and human factors. In this study, sediment cores were collected from human-planted mangroves in sub-tropical Ximen Island, China, and were determined for sedimentary phosphorus (P) species. The objective was to investigate the ability of mangroves planted in a zone bordering their temperature limit to preserve and regulate P. Our results showed that bioavailable P (BAP), which includes exchangeable-P (Ex-P), iron-bound P (Fe-P), and organic P (OP), accounted for approximately 64% of total P (TP). Apatite P (Ca-P), which accounted for 24% of TP, most likely originated from aquaculture activities surrounding the island. The vertical distribution of sedimentary P species along the sediment cores showed a rather constant trend along the salt marsh stand but considerable fluctuations for the mangroves and bare mudflat. These results indicate that mangroves accumulated P when there was a high P discharge event, and that this P was eventually released during organic matter decomposition and contributed to Ca-P formation. Nevertheless, old and young mangroves accumulated higher sedimentary P species, OP, and BAP compared to the salt marsh stand and bare mudflat areas. This study showed the potential of mangroves planted outside their suitable climate zone to preserve and regulate P.

Microbial mediators of plant community response to long-term N and P fertilization: Evidence of a role of plant responsiveness to mycorrhizal fungi

Climate changes and anthropogenic nutrient enrichment widely threaten plant diversity and ecosystem functions. Understanding the mechanisms governing plant species turnover across nutrient gradients is crucial to developing successful management and restoration strategies. We tested whether and how soil microbes, particularly arbuscular mycorrhizal fungi (AMF), could mediate plant community response to a 15 years long-term N (0, 4, 8, and 16 g N m^-2  year^-1 ) and P (0 and 8 g N m^-2  year^-1 ) enrichment in a grassland system. We found N and P enrichment resulted in plant community diversity decrease and composition change, in which perennial C₄  graminoids were dramatically reduced while annuals and perennial forbs increased. Metabarcoding analysis of soil fungal community showed that N and P changed fungal diversity and composition, of which only a cluster of AMF identified by the co-occurrence networks analysis was highly sensitive to P treatments and was negatively correlated with shifts in percentage cover of perennial C₄  graminoids. Moreover, by estimating the mycorrhizal responsiveness (MR) of 41 plant species in the field experiment from 264 independent tests, we found that the community weighted mean MR of the plant community was substantially reduced with nutrient enrichment and was positively correlated with C₄  graminoids percentage cover. Both analyses of covariance and structural equation modeling indicated that the shift in MR rather than AMF composition change was the primary predictor of the decline in perennial C₄  graminoids, suggesting that the energy cost invested by C₄ plants on those sensitive AMF might drive the inferior competitive abilities compared with other groups. Our results suggest that shifts in the competitive ability of mycorrhizal responsive plants can drive plant community change to anthropogenic eutrophication, suggesting a functional benefit of mycorrhizal mutualism in ecological restoration following climatic or anthropogenic degradation of soil communities.

Temporal and Spatial Analysis of Coastal Water Quality to Support Application of Whiteleg Shrimp Litopenaeus vannamei Intensive Pond Technology

The study aimed to determine the performance of whiteleg shrimp culture in relation to temporal and spatial aspects and characteristics and water quality status. Measurement and sampling of water were carried out before stocking/initial stocking of culture whiteleg shrimp (rainy season) and end of culture/after harvesting of whiteleg shrimp (dry season) at two locations in the coastal area of Bulukumba Regency, namely Bonto Bahari Subdistrict (BB) and Gantarang Subdistrict (GT), and one location as a control, namely in the coastal area of Ujung Loe Subdistrict. Variables measured and analyzed included temperature, salinity, pH, dissolved oxygen, nitrate, nitrite, ammonia, phosphate, total suspended solids, and total organic matter. Data were analyzed by descriptive statistics, multivariate statistics, and non-parametric statistics. Water quality status was determined using the Storet (Storage and Retrieval) method. The results showed that the culture of whiteleg shrimp was technology intensive with a stocking density of 110–220 ind/m2 with productivity between 13.9 and 44.4 tons/ha/cycle. The predicted waste load of N is 28.00 tons/cycle and P reaches 6.61 tons/cycle. Another result was that changes in water quality status during the rainy season were classified as moderately polluted at the BB location and complying with quality standards at the GT location. In the dry season, both locations were categorized as heavily polluted. Variables of water quality that caused the decrease in water quality status in both locations (BB and GT) were observed to increase salinity, nitrate concentration, and ammonia concentration and decreased dissolved oxygen concentration in the dry season. It is recommended to carry out proper feed management, use of probiotics, and increase the capacity and capability of wastewater treatment plants to reduce ammonia and nitrate concentrations in water in coastal areas. It is necessary to determine a more precise time for whiteleg shrimp stocking by reducing the possibility that whiteleg shrimp culture will still occur at the dry season’s peak.

Nitrogen addition promotes soil microbial beta diversity and the stochastic assembly

Nitrogen (N) deposition is one of major environmental concerns and alters the microbial communities in the pedosphere. A central debate in governing microbial community is on the relative importance of deterministic (ecological selection) vs. stochastic processes (dispersal, drift, diversification or speciation), which consequently limited our understanding of microbial assembly in response to N addition. Here, we conducted a global analysis of high-throughput sequencing data to reveal the mechanisms of N-addition effects on soil microbial communities. The results show that N addition significantly shifted the microbial community structure and promoted microbial beta diversity, particularly in the N-limited ecosystems. Changes in microbial structure and beta diversity increased significantly as the N addition rate, study duration, and the degree of soil acidification increased. The stochastic processes are more important than the deterministic processes for microbial community assembly, while N addition significantly increase the importance of stochastic processes whether the phylogenetic relationship is considered or not. Overall, the current study highlights the important of ecological stochasticity in regulating microbial assembly under N deposition scenarios.

Using integrated models to analyze and predict the variance of diatom community composition in an agricultural area

With the growing demand of assessing the ecological status, there is the need to fully understand the relationship between the planktic diversity and the environmental factors. Species richness and Shannon index have been widely used to describe the biodiversity of a community. Besides, we introduced the first ordination value from non-metric multidimensional scaling (NMDS) as a new index to represent the community similarity variance. In this study, we hypothesized that the variation of diatom community in rivers in an agricultural area was influenced by hydro-chemical variables. We collected daily mixed water samples using ISCO auto water samplers for diatoms and for water-chemistry analysis at the outlet of a lowland river for a consecutive year. An integrated modeling was adopted including random forest (RF) to decide the importance of the environmental factors influencing diatoms, generalized linear models (GLMs) combined with 10-folder cross validation to analyze and predict the diatom variation. The hierarchical analysis highlighted antecedent precipitation index (API) as the controlling hydrological variable while water temperature, Si²⁺ and PO₄-P as the main chemical controlling factors in our study area. The generalized linear models performed better prediction for Shannon index (R² = 0.44) and NMDS (R² = 0.51) than diatom abundance (R² = 0.25) and species richness (R² = 0.25). Our findings confirmed that Shannon index and the NMDS as an index showed good performance in explaining the relationship between stream biota and its environmental factors and in predicting the diatom community development based on the hydro-chemical predictors. Our study showed and highlighted the important hydro-chemical factors in the agricultural rivers, which could contribute to the further understanding of predicting diatom community development and could be implemented in the future water management protocol.

Enabling Biological Nitrogen Fixation for Cereal Crops in Fertilized Fields

Agricultural productivity relies on synthetic nitrogen fertilizers, yet half of that reactive nitrogen is lost to the environment. There is an urgent need for alternative nitrogen solutions to reduce the water pollution, ozone depletion, atmospheric particulate formation, and global greenhouse gas emissions associated with synthetic nitrogen fertilizer use. One such solution is biological nitrogen fixation (BNF), a component of the complex natural nitrogen cycle. BNF application to commercial agriculture is currently limited by fertilizer use and plant type. This paper describes the identification, development, and deployment of the first microbial product optimized using synthetic biology tools to enable BNF for corn (Zea mays) in fertilized fields, demonstrating the successful, safe commercialization of root-associated diazotrophs and realizing the potential of BNF to replace and reduce synthetic nitrogen fertilizer use in production agriculture. Derived from a wild nitrogen-fixing microbe isolated from agricultural soils, Klebsiella variicola 137-1036 ("Kv137-1036") retains the capacity of the parent strain to colonize corn roots while increasing nitrogen fixation activity 122-fold in nitrogen-rich environments. This technical milestone was then commercialized in less than half of the time of a traditional biological product, with robust biosafety evaluations and product formulations contributing to consumer confidence and ease of use. Tested in multi-year, multi-site field trial experiments throughout the U.S. Corn Belt, fields grown with Kv137-1036 exhibited both higher yields (0.35 ± 0.092 t/ha ± SE or 5.2 ± 1.4 bushels/acre ± SE) and reduced within-field yield variance by 25% in 2018 and 8% in 2019 compared to fields fertilized with synthetic nitrogen fertilizers alone. These results demonstrate the capacity of a broad-acre BNF product to fix nitrogen for corn in field conditions with reliable agronomic benefits.

Restoring Soil Fertility on Degraded Lands to Meet Food, Fuel, and Climate Security Needs via Perennialization

A continuously growing pressure to increase food, fiber, and fuel production to meet worldwide demand and achieve zero hunger has put severe pressure on soil resources. Abandoned, degraded, and marginal lands with significant agricultural constraints—many still used for agricultural production—result from inappropriately intensive management, insufficient attention to soil conservation, and climate change. Continued use for agricultural production will often require ever more external inputs such as fertilizers and herbicides, further exacerbating soil degradation and impeding nutrient recycling and retention. Growing evidence suggests that degraded lands have a large potential for restoration, perhaps most effectively via perennial cropping systems that can simultaneously provide additional ecosystem services. Here we synthesize the advantages of and potentials for using perennial vegetation to restore soil fertility on degraded croplands, by summarizing the principal mechanisms underpinning soil carbon stabilization and nitrogen and phosphorus availability and retention. We illustrate restoration potentials with example systems that deliver climate mitigation (cellulosic bioenergy), animal production (intensive rotational grazing), and biodiversity conservation (natural ecological succession). Perennialization has substantial promise for restoring fertility to degraded croplands, helping to meet future food security needs.

Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems

Our current understanding of enzymatic polysaccharide degradation has come from a huge number of in vitro studies with purified enzymes. While this vast body of work has been invaluable in identifying and characterizing novel mechanisms of action and engineering desirable traits into these enzymes, a comprehensive picture of how these enzymes work as part of a native in vivo system is less clear. Recently, several model bacteria have emerged with genetic systems that allow for a more nuanced study of carbohydrate active enzymes (CAZymes) and how their activity affects bacterial carbon metabolism. With these bacterial model systems, it is now possible to not only study a single nutrient system in isolation (i.e., carbohydrate degradation and carbon metabolism), but also how multiple systems are integrated. Given that most environmental polysaccharides are carbon rich but nitrogen poor (e.g., lignocellulose), the interplay between carbon and nitrogen metabolism in polysaccharide-degrading bacteria can now be studied in a physiologically relevant manner. Therefore, in this review, we have summarized what has been experimentally determined for CAZyme regulation, production, and export in relation to nitrogen metabolism for two Gram-positive (Caldicellulosiruptor bescii and Clostridium thermocellum) and two Gram-negative (Bacteroides thetaiotaomicron and Cellvibrio japonicus) polysaccharide-degrading bacteria. By comparing and contrasting these four bacteria, we have highlighted the shared and unique features of each, with a focus on in vivo studies, in regard to carbon and nitrogen assimilation. We conclude with what we believe are two important questions that can act as guideposts for future work to better understand the integration of carbon and nitrogen metabolism in polysaccharide-degrading bacteria. KEY POINTS: • Regardless of CAZyme deployment system, the generation of a local pool of oligosaccharides is a common strategy among Gram-negative and Gram-positive polysaccharide degraders as a means to maximally recoup the energy expenditure of CAZyme production and export. • Due to the nitrogen deficiency of insoluble polysaccharide-containing substrates, Gram-negative and Gram-positive polysaccharide degraders have a diverse set of strategies for supplementation and assimilation. • Future work needs to precisely characterize the energetic expenditures of CAZyme deployment and bolster our understanding of how carbon and nitrogen metabolism are integrated in both Gram-negative and Gram-positive polysaccharide-degrading bacteria, as both of these will significantly influence a given bacterium's suitability for biotechnology applications.

Exploring environmental selection on genome size in angiosperms

Angiosperms show a remarkable range in genome size (GS), yet most species have small genomes, despite the frequency of polyploidy and repeat amplification in the ancestries of most lineages. It has been suggested that larger genomes incur costs that have driven selection for GS reduction, although the nature of these costs and how they might impact selection remain unclear. We explore potential costs of increased GS encompassing impacts on minimum cell size with consequences for photosynthesis and water-use efficiency and effects of greater nitrogen and phosphorus demands of the nucleus leading to more severe trade-offs with photosynthesis. We suggest that nutrient-, water-, and/or CO₂-stressed conditions might favour species with smaller genomes, with implications for species' ecological and evolutionary dynamics.

Legume-rhizobium dance: an agricultural tool that could be improved?

The specific interaction between rhizobia and legume roots leads to the development of a highly regulated process called nodulation, by which the atmospheric nitrogen is converted into an assimilable plant nutrient. This capacity is the basis for the use of bacterial inoculants for field crop cultivation. Legume plants have acquired tools that allow the entry of compatible bacteria. Likewise, plants can impose sanctions against the maintenance of nodules occupied by rhizobia with low nitrogen-fixing capacity. At the same time, bacteria must overcome different obstacles posed first by the environment and then by the legume. The present review describes the mechanisms involved in the regulation of the entire legume-rhizobium symbiotic process and the strategies and tools of bacteria for reaching the nitrogen-fixing state inside the nodule. Also, we revised different approaches to improve the nodulation process for a better crop yield.

Benefits of phosphate solubilizing bacteria on belowground crop performance for improved crop acquisition of phosphorus

Although research on plant growth promoting bacteria began in the 1950s, basic and applied research on bacteria improving use of phosphorus (P) continues to be a priority among many agricultural research institutions. Ultimately, identifying agriculturally beneficial microbes, notably P solubilizing bacteria (PSB), that enhance the efficient use of P supports more sustainable cropping systems and the judicious use of mineral nutrients. In parallel, there is more attention on improving crop root P acquisition of existing soil P pools as well as by increasing the proportion of fertilizer P that is taken up by crops. Today, new lines of research are emerging to investigate the co-optimization of PSB-fertilizer-crop root processes for improved P efficiency and agricultural performance. In this review, we compile and summarize available findings on the beneficial effects of PSB on crop production with a focus on crop P acquisition via root system responses at the structural, functional and transcriptional levels. We discuss the current state of knowledge on the mechanisms of PSB-mediated P availability, both soil- and root-associated, as well as crop uptake via P solubilization, mineralization and mobilization, mainly through the production of organic acids and P-hydrolyzing enzymes, and effects on phytohormone signaling for crop root developement. The systematic changes caused by PSB on crop roots are discussed and contextualized within promising functional trait-based frameworks. We also detail agronomic profitability of P (mineral and organic) and PSB co-application, in amended soils and inoculated crops, establishing the connection between the influence of PSB on agroecosystem production and the impact of P fertilization on microbial diversity and crop functional traits for P acquisition.

Influences of pesticides, nutrients, and local environmental variables on phytoplankton communities in lentic small water bodies in a German lowland agricultural area

Agrochemicals such as pesticides and nutrients are concurrent chemical stressors in freshwater aquatic ecosystems surrounded by agricultural areas. Lentic small water bodies (LSWB) are ecologically significant habitats especially for maintaining biodiversity but highly understudied. Phytoplankton are ideal indicator species for stress responses. Functional features of the phytoplankton are important in revealing the processes that determine the structure of the communities. In this study, we investigated the effects of pesticides, nutrients, and local environmental variables on the species composition and functional features of phytoplankton communities in LSWB. We studied pesticide toxicity of ninety-four pesticides, three nutrients (NH₄-N, NO₃-N and PO₄-P) and local environment variables (precipitation, water level change, temperature, dissolved oxygen concentration, electrical conductivity, pH) in five LSWB over twelve weeks during the spring pesticide application period. We explored respective changes in species composition of phytoplankton community and functional features. Redundancy analysis and variance partitioning analysis were applied to correlate phytoplankton community compositions with the pesticide toxicity (as maximum toxicity in toxic units), nutrients and local environment variables. We used multiple linear regression models to identify the main environmental variables driving the functional features of phytoplankton communities. Pesticide toxicity, nutrients and local environmental variables significantly (p < 0.001) contributed to shaping phytoplankton community composition individually. Local environment variables showed the highest pure contribution for driving phytoplankton composition (12%), followed by nutrients (8%) and pesticide toxicity (2%). Functional features (represented by functional diversity and functional redundancy) of the phytoplankton community were significantly affected by pesticide toxicity and nutrients concentrations. The functional richness and functional evenness were negatively affected by PO₄-P concentrations. Pesticide toxicity was positively correlated with functional redundancy indices. Our findings emphasized the relative importance of concurrent multiple stressors (e.g., pesticides and nutrients) on phytoplankton community structure, directing potential effects on metacommunity structures in aquatic ecosystems subjected to agricultural runoff.