Incorporating adaptive genomic variation into predictive models for invasion risk assessment

Global climate change is expected to accelerate biological invasions, necessitating accurate risk forecasting and management strategies. However, current invasion risk assessments often overlook adaptive genomic variation, which plays a significant role in the persistence and expansion of invasive populations. Here we used Molgula manhattensis, a highly invasive ascidian, as a model to assess its invasion risks along Chinese coasts under climate change. Through population genomics analyses, we identified two genetic clusters, the north and south clusters, based on geographic distributions. To predict invasion risks, we employed the gradient forest and species distribution models to calculate genomic offset and species habitat suitability, respectively. These approaches yielded distinct predictions: the gradient forest model suggested a greater genomic offset to future climatic conditions for the north cluster (i.e., lower invasion risks), while the species distribution model indicated higher future habitat suitability for the same cluster (i.e, higher invasion risks). By integrating these models, we found that the south cluster exhibited minor genome-niche disruptions in the future, indicating higher invasion risks. Our study highlights the complementary roles of genomic offset and habitat suitability in assessing invasion risks under climate change. Moreover, incorporating adaptive genomic variation into predictive models can significantly enhance future invasion risk predictions and enable effective management strategies for biological invasions in the future.

Temporal assembly patterns of microbial communities in three parallel bioreactors treating low-concentration coking wastewater with differing carbon source concentrations

Carbon source is an important factor of biological treatment systems, the effects of which on their temporal community assembly patterns are not sufficiently understood currently. In this study, the temporal dynamics and driving mechanisms of the communities in three parallel bioreactors for low-concentration coking wastewater (CWW) treatment with differing carbon source concentrations (S0 with no glucose addition, S1 with 200 mg/L glucose addition and S2 with 400 mg/L glucose addition) were comprehensively studied. High-throughput sequencing and bioinformatics analyses including network analysis and Infer Community Assembly Mechanisms by Phylogenetic bin-based null model (iCAMP) were used. The communities of three systems showed turnover rates of 0.0029∼0.0034 every 15 days. Network analysis results showed that the S0 network showed higher positive correlation proportion (71.43%) and clustering coefficient (0.33), suggesting that carbon source shortage in S0 promoted interactions and cooperation of microbes. The neutral community model analysis showed that the immigration rate increased from 0.5247 in S0 to 0.6478 in S2. The iCAMP analysis results showed that drift (45.89%) and homogeneous selection (31.68%) dominated in driving the assembly of all the investigated microbial communities. The contribution of homogeneous selection increased with the increase of carbon source concentrations, from 27.92% in S0 to 36.08% in S2. The OTUs participating in aerobic respiration and tricarboxylic acid (TCA) cycle were abundant among the bins mainly affected by deterministic processes, while those related to the metabolism of refractory organic pollutants in CWW such as alkanes, benzenes and phenols were abundant in the bins dominated by stochastic processes.

Defining nutrient ecoregions for reference nitrogen and phosphorus concentrations in rivers from the major South American biomes

Delineating reference (i.e., baseline) riverine nutrient concentrations is essential to understand fundamental processes of biogeochemical transport from continents to the ocean, describe ecological conditions, and inform managers of best attainable conditions when attempting to control anthropogenic eutrophication. We used data from 434 Brazilian watersheds representative of major South American biomes covering over half the continental area, to estimate nutrient levels expected prior to anthropogenic development. We used a novel watershed-based approach to describe spatial patterns throughout Brazil and for the entire Amazon basin. This approach considered nitrogen (N) and phosphorus (P) independently and allowed removal of anthropogenic influences. The approach was useful where there were few unimpacted watersheds and low levels of urbanization had strong effects. We found reference total N concentrations were most closely related to biome, whereas total P levels related to percentage sand in soils in addition to climatic features influencing biomes. There was a wide range of N:P at this coarse level, suggesting P or co-limitation could occur in streams; many areas have intrinsically high background P and relatively low N, suggesting N-limitation of freshwaters could be widespread in South America, favoring nitrogen-fixing cyanobacterial blooms. We provide unique broad-scale analyses of spatial distribution of baseline nutrient levels for tropical and subtropical watersheds across continental scales.

A new strategy for optimizing marine protection networks by considering functional connectivity: An example of Tachypleus tridentatus

The concept of creating a conservation network through the establishment of multiple protected areas to protect marine fauna is gaining momentum. To effectively establish a network that yields favorable outcomes, it is imperative to identify suitable areas that foster optimal connectivity. Given the swift development of coastal areas, it has become necessary to develop cost-effective measures that yield maximum conservation benefits. However, exploration of these ideas for application to marine conservation networks remains scarce. In this study, we used the horseshoe crab (Tachypleus tridentatus) in the Beibu Gulf as an example. The species and environmental data were collected through field sampling and remote sensing. The species distribution model, the least-cost path model, and circuit theory were employed to establish a marine conservation network. The functional connectivity metrics were employed to optimize both the interconnection and economic efficiency of the network. The results indicated a low presence of adult horseshoe crabs in the Beibu Gulf, with average densities of 1.47 and 1.43 ind./km2 among the 38 surveyed stations in 2018 and 2019, respectively. The species distribution model accurately predicted juvenile presence in mudflats and adult presence offshore, and it identified 43 potential areas that are suitable for the establishment of marine protected areas. The marine protected areas that ranked higher in importance contributed significantly to maintaining the integrity of regional connectivity. The network connectivity shows a law of diminishing returns as the number of marine protected areas increases. The framework developed in this study will provide decision support for building and optimizing marine conservation networks.

Mysterious Bamboo flowering phenomenon: A literature review and new perspectives

Bamboo, a globally distributed non-timber forest resource, plays a critical role in local ecosystems and economies. Despite its significance, the understanding of bamboo's long and unpredictable flowering cycles remains limited. Our bibliometric analysis of bamboo flowering-related literature from the Web of Science database reveals an initial focus on regeneration studies, with a recent trend shifting towards microscopic and molecular perspectives. Furthermore, our narrative review emphasizes the importance of considering factors such as the proportion of flowering culms and the duration of flowering in classifying bamboo flowering phenomena. While numerous studies have endorsed the predator saturation hypothesis as a suitable explanation for the synchronicity of bamboo flowering, no existing theory explains bamboo's prolonged flowering cycles. We propose a new natural selection hypothesis as a potential explanation for these extraordinary cycles, underscoring the need for further research in this area. Despite the substantial volume of data accumulated on bamboo flowering, these resources have not been fully exploited in recent research. Future studies would benefit from more comprehensive data collection methods, encompassing field observations, satellite remote sensing data, and omics data. The convergence of traditional ecological studies with molecular techniques may pave the way for significant advancements in bamboo flowering research.

Effects of simulated warming on soil microbial community diversity and composition across diverse ecosystems

Soil warming can directly affect the microbial community, or indirectly affect the microbial community by affecting soil moisture, nutrient availability, vegetation growth, etc. However, the response of microorganisms to soil warming is complex, and there is no uniform conclusion on the impact and mechanism of warming on microbial diversity. As the global climate gradually warms, a comprehensive assessment of warming on soil microbial community changes is essential to understand and predict the response of microbial geochemical processes to soil warming. Here, we perform a meta-analysis of studies to investigate changes in soil microbial communities along soil warming gradients and the response of soil microbes to elevated temperature in different ecosystems. We found that the α diversity index of soil microorganisms decreased significantly with the increase in temperature, and the β diversity altered with the increase in soil temperature and the shifts in ecosystem. Most bacteria only alter when the temperature rises higher. Compared to the non-warming condition, the relative abundance of Acidobacteria, Proteobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia decreased by 19 %, 11 %, 19 %, 8 % and 6 %, respectively, and the relative abundance of Firmicutes increased by 34 %. Compared to farmland, forest, grassland and tundra ecosystems, soil microorganisms in wetland ecosystems were more sensitive to temperature increase, and the changes in bacteria were consistent with the overall alterations. This meta-analysis revealed significant changes in the composition of microbial communities on soil warming. With the decrease in biodiversity under increasing temperature conditions, these dominant microbiomes, which can grow well under high-temperature conditions, will play a stronger role in regulating nutrient and energy flow. Our analysis adds a global perspective to the temperature response of soil microbes, which is critical to improving our understanding of the mechanisms of how soil microbes change in response to climate warming.

Effect of acetochlor on the symbiotic relationship between microalgae and bacteria

In this study, two strains of symbiotic bacteria (SOB-1 and SOB-2) were isolated from Scenedesmus obliquus, and various algal-bacterial mutualistic systems were established under acetochlor (ACT) stress conditions. Following exposure to varying ACT concentrations from 2.0 to 25.0 μg/L, the capacity for co-cultured bacteria to degrade ACT was enhanced in 7 days by up to 226.9% (SOB-1) and 193.0% (SOB-2), compared with axenic algae, although bacteria exposed to higher ACT concentrations exacerbated algal metabolic stress, oxidative states, apoptosis and cellular lysis. ACT reduced carbohydrates in the phycosphere by up to 31.5%; compensatory nutrient plunder and structural damage by bacteria were the potential exploitation pathways determined based on the inhibition of bacterial infection using a glucanase inhibitor. The ACT-induced reduction in algal antimicrobial substances, including fatty acids and phenolics (by up to 58.1% and 56.6%, respectively), also facilitated bacterial exploitation of algae. ACT-dependent interspecific interaction coefficients between algae and bacteria generated from long-term symbiosis cultures implied that bacteria moved from mutualism (0 and 2.0 μg/L ACT) to exploitation (7.9 and 25.0 μg/L ACT). The population dynamic model under incremental ACT-concentration scenarios inferred that theoretical systematic extinction may occur in algal-bacterial systems earlier than in axenic algae. These outcomes provide interspecific insights into the distortion of algal-bacterial reciprocity due to the ecotoxicological effects of ACT.

Elevated CO2 increases soil redox potential by promoting root radial oxygen loss in paddy field

Soil redox potential (Eh) plays an important role in the biogeochemical cycling of soil nutrients. Whereas its effect soil process and nutrients' availability under elevated atmospheric CO2 concentration and warming has seldom been investigated. Thus, in this study, a field experiment was used to elucidate the effect of elevated CO2 concentration and warming on soil Eh, redox-sensitive elements and root radial oxygen loss (ROL). We hypothesized elevated CO2 and warming could alter soil Eh by promoting or inhibiting ROL. We found that soil Eh in the rhizosphere was significantly higher than that of non-rhizosphere. Elevated CO2 enhanced soil Eh by 11.5%, which corresponded to a significant decrease in soil Fe2+ and Mn2+concentration. Under elevated CO2, the concentration of Fe2+ and Mn2+ decreased by 14.7% and 13.7%, respectively. We also found that elevated CO2 altered rice root aerenchyma structure and promoted rice root ROL. Under elevated CO2, rice root ROL increased by 79.5% and 112.2% for Yangdao 6 and Changyou 5, respectively. Warming had no effect on soil Eh and rice root ROL. While warming increased the concentration of Mn2+ and SO42- by 4.9% and 19.3%, respectively. There was a significant interaction between elevated CO2 and warming on Fe2+ and Mn2+. Under elevated CO2, warming had no effect on the concentration of Fe2+ but decreased Mn2+ concentration significantly. Our study demonstrated that elevated atmospheric CO2 in the future could increase soil Eh by promoting rice root ROL, which will alter some soil nutrients' availability, such as Fe2+ and Mn2+.

Livestock grazing and biodiversity: Effects on CO2 exchange in semi-arid Karoo ecosystems, South Africa

Livestock use in semi-arid South African ecosystems has not been extensively studied in relation to the Net Ecosystem Exchange (NEE) of carbon dioxide (CO2). We present four years of measurements from twinned eddy-covariance towers in Nama-Karoo, South Africa, to investigate the carbon fluxes and the impact of grazing intensity on NEE. The design contrasted NEE at a long-term site grazed at recommended levels (LG) with a long-term heavily grazed (EG) site that had been rested for 10 years, and was monitored for two years after which intensive grazing was reintroduced for this experiment. This allowed for the quantification of long-term NEE trends on "recovering" vegetations (years I, II) and short-term responses to an intensified land use (years III, IV). The results showed that the net release of CO2 was slightly higher at LG than on "recovering" vegetation at the EG site, where near-neutral exchange was observed during years I and II. However, after grazing was reintroduced to the EG site, differences between sites was reduced but not eliminated. These findings suggest that there is a somewhat higher carbon sequestration potential at the resting EG site than at the LG site, apparently associated with the dominance of unpalatable drought-tolerant grass species and local elimination of many palatable shrubs. Reduction of this sink potential by reintroduction of high-intensity grazing indicates the sensitivity of C-sequestration in this "recovering" system to heavy grazing, but underlines continued resilience of NEE under far heavier grazing than in the LG system. These data suggest notable trade-offs in these ecosystems between carbon storage, biodiversity, and livestock production with rainfall variability being a critical inter-annual driver. PLAIN LANGUAGE SUMMARY: This study suggests that long-term resting of previously over-utilized southern African semi-arid vegetation supports enhanced carbon sequestration potential, even if over-utilization has transformed vegetation composition (i.e. has caused degradation through reduced plant species richness). However, this enhanced carbon sequestration potential can be quickly negated by the reintroduction of grazing, even after 10 years of resting. Achievement of carbon sequestration is dependent on average to above-average precipitation and its distribution throughout the year, with sink activity evident mainly after seasonal rains during the warm season.

Isotopic characteristics and source analysis of atmospheric ammonia during agricultural periods in the Xichuan area of the Danjiangkou Reservoir

Nitrogen deposition is an important means of exogenous nitrogen input in reservoir water. Agricultural activities around the reservoir lead to a sharp increase in the concentration of ammonia in the atmosphere, which poses a threat to the reservoir water body. Clarifying the contribution of agricultural ammonia release to atmospheric NHx (gaseous NH3 and particulate NH4+), in the reservoir area can provide a theoretical foundation for local reactive nitrogen control. We collected atmospheric NH3 and NH4+ samples during the agricultural periods and analyzed the isotopic characteristics of atmospheric NHx and the contribution rates of different ammonia sources in the Xichuan area of the Danjiangkou Reservoir. The results showed that the initial δ15N values of NH3 (-30.0‰ to -7.2‰) and particulate NH4+(-33‰ to +4.9‰ for finer and coarser particles, respectively) are different, and their contribution ratios from dissimilar ammonia sources are also different, among which NH4+ is more susceptible to meteorological factors. However, since the atmospheric NHx in the Xichuan area is mainly gaseous NH3, the final sources of atmospheric ammonia nitrogen source depend on gaseous NH3. Agricultural sources (59%-74%) were the main NH3 sources in this area. Among them, the fertilizer use emission was dominant; it had the highest contribution rate in summer during the agricultural period and a more prominent impact in areas with less human interference. Reasonable regulation of the application of high-ammonia releasing fertilizer, especially during the agricultural period in summer, is an effective way to reduce the threat of atmospheric ammonia to water health.

Intergenerational consequences of an auxin-like herbicide on plant sensitivity to a graminicide mediated by a fungal endophyte

In agroecosystems, herbicides are the predominant anthropogenic selection pressure for agriculture weed species. While weeds are the primary target, herbicides can have adverse impacts on non-target plant beneficial microorganisms. We aimed to investigate the influence of a foliar endophytic fungus (Epichloë occultans) on the sensitivity of Lolium multiflorum to a graminicide herbicide (diclofop-methyl) during both plant ontogeny and progeny. Susceptible individuals to diclofop-methyl with and without endophyte were pre-exposed to the auxin 2,4-D herbicide. This herbicide is known to stimulate the metabolic detoxification mechanism (CYP-450) of diclofop-methyl. Regardless of the endophyte, 2,4-D pre-treatment increased mother plant survival to nearly 100 % under diclofop treatment but not in the progeny. Furthermore, maternal plant exposure to 2,4-D reduced endophyte transmission to the seeds and from seed-to-seedlings. Our findings suggest that, despite a reduction in diclofop-methyl sensitivity during the ontogeny of mother plants, 2,4-D-mediated induction of likely CYP-450 metabolism is not intergenerationally transmitted and shows detrimental effects on the symbiotic endophyte persistence.

Light-dark fluctuated metabolic features of diazotrophic and non-diazotrophic cyanobacteria and their coexisting bacteria

Cyanobacteria, the most abundant photosynthetic organisms in oceans, are tightly associated with diverse microbiota. However, the relationships between heterotrophic bacteria and cyanobacteria, particularly the diazotrophic group, are not fully understood. Here, we compared diel gene expressions of N2 fixing cyanobacteria Crocosphaera watsonii WH0003 and non-diazotrophic Synechococcus sp. RS9902 and their associated bacteria using metatranscriptomics approach. WH0003 showed significant up-regulation of O2 restriction and oxidative phosphorylation related genes at nighttime due to large carbon and energy investments for active N2 fixation. In contrast, RS9902 had higher expression for those genes at daytime. The two cyanobacteria hosted distinct bacterial communities with clear separate substrate utilization niches to reduce competition. Light-dark partitioning of nutrient acquisition among the dominant bacterial groups likely contributed to the dynamic balance for community coexistence. Moreover, particle-attached (PA) bacteria in RS9902 largely expressed glycoside hydrolases to hydrolyze complex carbohydrate compounds, while free-living (FL) bacteria priorly assimilated soluble, diffusible molecules. Spatial partitioning of nutrient acquisition between PA and FL bacteria implied that location initially influenced metabolic features of host associated bacteria. Our results advance knowledge on light-dark regulated metabolic activities of diazotrophic and non-diazotrophic cyanobacteria, and provide new insights into the coexisting strategies of different bacterial groups.