Microeukaryotic plankton community dynamics under ecological water replenishment: Insights from eDNA metabarcoding

Ecological water replenishment (EWR) is an important strategy for river restoration globally, but timely evaluation of its ecological effects at a large spatiotemporal scale to further adjust the EWR schemes is of great challenge. Here, we examine the impact of EWR on microeukaryotic plankton communities in three distinct river ecosystems through environmental DNA (eDNA) metabarcoding. The three ecosystems include a long-term cut-off river, a short-term connected river after EWR, and long-term connected rivers. We analyzed community stability by investigating species composition, stochastic and deterministic dynamics interplay, and ecological network robustness. We found that EWR markedly reduced the diversity and complexity of microeukaryotic plankton, altered their community dynamics, and lessened the variation within the community. Moreover, EWR disrupted the deterministic patterns of community organization, favoring dispersal constraints, and aligning with trends observed in naturally connected rivers. The shift from an isolated to a temporarily connected river appeared to transition community structuring mechanisms from deterministic to stochastic dominance, whereas, in permanently connected rivers, both forces concurrently influenced community assembly. The ecological network in temporarily connected rivers post-EWR demonstrated significantly greater stability and intricacy compared to other river systems. This shift markedly bolstered the resilience of the ecological network. The eDNA metabarcoding insights offer a novel understanding of ecosystem resilience under EWR interventions, which could be critical in assessing the effects of river restoration projects throughout their life cycle.

Construction of ecological network in Qujing city based on MSPA and MCR models

With the rapid advancement of urbanization and industrialization, ecological patches within cities and towns are fragmented and ecological corridors are cut off, regional ecological security is threatened and sustainable development is hindered. Building an ecological network that conforms to regional realities can connect fragmented patches, protect biodiversity and regional characteristics, and provide scientific reference for regional ecological protection and ecological network planning. By taking Qilin District, the main urban area of Qujing City as an example, and using geospatial data as the main data source, based on morphological spatial pattern analysis (MSPA) and minimum cumulative resistance (MCR), this study identified ecological source areas, extracted ecological corridors, and build & optimize ecological networks. (1) All landscape types are identified based on MSPA, the proportion of core area was the highest among all landscape types, which was 80.69%, combined with the connectivity evaluation, 14 important ecological source areas were selected. (2) 91 potential ecological corridors were extracted through MCR and gravity models, there were 16 important ones. (3) The network connectivity analysis method is used to calculate the α, β, and γ indexes of the ecological network before optimization, which were 2.36, 6.5, and 2.53, while after optimization, α, β and γ indices were 3.8, 9.5 and 3.5, respectively. The combined application of MSPA-MCR model and ecological network connectivity analysis evaluation is conducive to improving the structure and functionality of ecological network.

Multiplex dependence analysis of China's interprovincial virtual water based on an ecological network

The interprovincial circulation of goods and services has formed virtual water flows between regions, which can redistribute water resources. Based on previous virtual water trade research, this study further explored the multiple dependencies of virtual water, i.e., direct, indirect, and complete dependence. This study examined the direct, indirect, and complete dependence of virtual water between provinces in China by constructing multilayer dependence networks and identified the key regions and paths of virtual water trade network. The results showed direct dependence was the densest and had the largest overall dependence degree, but indirect dependence was the most stable and orderly. Second, the dominant provinces were Guangxi, Hunan, Sichuan, Xinjiang, and Anhui, referred to as "core‒five‒region," and the flow relevant to them accounted for approximately 30% of the virtual water. The seven provinces of Shanxi, Zhejiang, Shandong, Hubei, Guangdong, Shaanxi, and Gansu depend both directly and indirectly on the "core‒five‒region." Shanxi and Zhejiang have close direct and indirect dependence, with more than one of the "core‒five‒region." Guangdong was the province with the most direct and indirect input of virtual water from the "core‒five‒region." The study provides a scientific basis for multiregional identification for the collaborative management of water resources in China from the perspective of dependence.

New insights into substrates shaped nutrients removal, species interactions and community assembly mechanisms in tidal flow constructed wetlands treating low carbon-to-nitrogen rural wastewater

A limited understanding of microbial interactions and community assembly mechanisms in constructed wetlands (CWs), particularly with different substrates, has hampered the establishment of ecological connections between micro-level interactions and macro-level wetland performance. In this study, CWs with distinct substrates (zeolite, CW_A; manganese ore, CW_B) were constructed to investigate the nutrient removal efficiency, microbial interactions, metabolic mechanisms, and ecological assembly for treating rural sewage with a low carbon-to-nitrogen ratio. CW_B showed higher removal of ammonia nitrogen and total nitrogen by about 1.75-6.75 % and 3.42-5.18 %, respectively, compared to CW_A. Candidatus_Competibacter (denitrifying glycogen-accumulating bacteria) was the dominant microbial genus in CW_A, whereas unclassified_f_Blastocatellaceae (involved in carbon and nitrogen transformation) dominated in CW_B. The null model revealed that stochastic processes (drift) dominated community assembly in both CWs; however, deterministic selection accounted for a higher proportion in CW_B. Compared to those in CW_A, the interactions between microbes in CW_B were more complex, with more key microbes involved in carbon, nitrogen, and phosphorus conversion; the synergistic cooperation of functional bacteria facilitated simultaneous nitrification-denitrification. Manganese ores favour biofilm formation, increase the activity of the electron transport system, and enhance ammonia oxidation and nitrate reduction. These results elucidated the ecological patterns exhibited by microbes under different substrate conditions thereby contributing to our understanding of how substrates shape distinct microcosms in CW systems. This study provides valuable insights for guiding the future construction and management of CWs.

Microbial functional heterogeneity induced in a petroleum-polluted soil profile

Microbial taxonomic diversity declines with increasing stress caused by petroleum pollution. However, few studies have tested whether functional diversities vary similarly to taxonomic diversity along the stress gradient. Here, we investigated soil microbial communities in a petrochemically polluted site in China. Total petroleum hydrocarbon (TPH) concentrations were higher in the middle (2-3 m) and deep soil layer (3-5 m) than in the surface soil layer (0-2 m). Accordingly, microbial taxonomic α-diversity was decreased by 44% (p < 0.001) in the middle and deep soil layers, compared to the surface soil layer. In contrast, functional α-diversity decreased by 3% (p < 0.001), showing a much better buffering capacity to environmental stress. Differences in microbial taxonomic and functional β-diversities were enlarged in the middle and deep soil layers, extending the Anna Karenina Principle (AKP) that a community adapts to stressful environments in its own way. Consistent with the stress gradient hypothesis, we revealed a higher degree of network connectivity among microbial species and genes in the middle and deep soil layers compared to the surface soil layer. Together, we demonstrate that microbial functionality is more tolerant to stress than taxonomy, both of which were amenable to AKP and the stress gradient hypothesis.

Response of soil micro-food web to nutrient limitation along a subtropical forest restoration

Forest ecosystem productivity and function is strongly influenced by the interaction between soil organisms and their resource use that can be impeded by an imbalance of ecological stoichiometry. Soil microorganisms are known to have an important role in biogeochemical cycling which is strongly influenced by ecological stoichiometry. However, there is limited understanding of how soil micro-food web respond to stoichiometric imbalances during forest restoration. Here, we investigated the effect of forest restoration on soil physio-chemical properties and the structure and function of soil micro-food web along a chronosequence of transformation stages: (i) early stage monoculture plantation of Chinese fir (Cunninghamia lanceolata) comprised of three age classes (5, 10 and 20 years); (ii) mid-stage conifer-broadleaved mixed forest; and (iii) late-stage mixed species broadleaved forest in south China. Results showed that forest restoration from C. lanceolata monocultures to mixed species broadleaved forest significantly increased soil organic carbon and total nitrogen. Soil bacteria, fungi, protists and nematodes abundance increased and the co-occurrence networks of soil biota became more complex and stable along the restoration chronosequence. In contrast, soil nitrogen and phosphorus limitations, particularly phosphorus limitation, increased along the chronosequence. In addition, soil exoenzyme activity suggested that the microbial investment in resource acquisition shifted from C- to nutrient-acquiring enzymes from the earlier to the later restoration stages. Availability of soil resources (e.g., dissolved organic carbon, ammonium, and available phosphate) appeared to have an important role in regulating soil food web composition, structure and stability during forest restoration. We conclude that nutrient limitation, particularly phosphorus limitation, likely has an important role in determining the stability of soil food webs during forest restoration. These findings contribute to our understanding of the relationships between soil nutrient limitation and soil micro-food web, and have implications for carbon sequestration through forest restoration and management in southern China.

Effects of polyethylene microplastics and heavy metals on soil-plant microbial dynamics

Polyethylene (PE) microplastics are emerging pollutants that pose a significant threat to the environment and human health. However, little is known about the effects of PEs on soil‒plant interactions, especially in heavy metal (HM)-contaminated soil. In this study, the effects of PE on rhizosphere soil enzyme activities, microbial interactions and nutrient cycling processes were analyzed from ecological network and functional gene perspectives for the first time. The results indicated that PE-MP addition significantly reduced the biomass of Bidens pilosa L. In addition, the partial increase in carbon, nitrogen, and phosphorus enzyme activities suggested that the effects of PE as a carbon source on microbial functions in HM-contaminated soil should not be ignored. The average path length of bacterial network nodes was found to be higher than that of fungal network nodes, demonstrating that the bacterial ecological network in PE-MP and HM cocontaminated environments has good buffering capacity against changes in external environmental conditions. Furthermore, structural equation modeling demonstrated that particle size and dosage affect soil nutrient cycling processes and that cycling processes are acutely aware of changes in any factor, such as soil moisture, soil pH and soil nitrogen nutrients. Hence, PE-MP addition in HM-contaminated soil has the potential to alter soil ecological functions and nutrient cycles.

Tetracycline inhibits the nitrogen fixation ability of soybean (Glycine max (L.) Merr.) nodules in black soil by altering the root and rhizosphere bacterial communities

Tetracycline is a widely used antibiotic and may thus also be an environmental contaminant with an influence on plant growth. The aim of this study was to investigate the inhibition mechanisms of tetracycline in relation to soybean growth and ecological networks in the roots and rhizosphere. To this end, we conducted a pot experiment in which soybean seedlings were grown in soil treated with 0, 10, or 25 mg/kg tetracycline. The effects of tetracycline pollution on growth, productivity, oxidative stress, and nitrogenase activity were evaluated. We further identified the changes in microbial taxa composition and structure at the genus and species levels by sequencing the 16S rRNA gene region. The results showed that tetracycline activates the antioxidant defense system in soybeans, which reduces the abundance of Bradyrhizobiaceae, inhibits the nitrogen-fixing ability, and decreases the nitrogen content in the root system. Tetracycline was also found to suppress the formation of the rhizospheric environment and decrease the complexity and stability of bacterial networks. Beta diversity analysis showed that the community structure of the root was markedly changed by the addition of tetracycline, which predominantly affected stochastic processes. These findings demonstrate that the influence of tetracycline on soybean roots could be attributed to the decreased stability of the bacterial community structure, which limits the number of rhizobium nodules and inhibits the nitrogen-fixing capacity. This exploration of the inhibitory mechanisms of tetracycline in relation to soybean root development emphasises the potential risks of tetracycline pollution to plant growth in an agricultural setting. Furthermore, this study provides a theoretical foundation from which to improve our understanding of the physiological toxicity of antibiotics in farmland.

Insight into microbial functional genes' role in geochemical distribution and cycling of uranium: The evidence from covering soils of uranium tailings dam

There exists a research gap on microbial functional genes' role in U geochemical behavior and cycling in U contaminated soils, which has been poorly understood. Herein, 16S rRNA sequencing gene amplifiers and metagenome analysis were applied to probe microbial community structure and functional metabolism of different depth layers of covering soils in U tailings dam. Results showed that the soils were highly enriched with U (47.5-123.3 mg/kg) and a remarkable portion of 35-70% was associated with the labile fractions. It was found that U geochemical distribution was notably interacted with functional genes from N, S, Fe and P related microbes. Importantly, diminution in gene NirK and amplification in nrfH involving in nitrate reduction could induce microbial tolerance to U. Moreover, gene Sat in microbial sulfate reduction, NosZ and NorB in nitrate reduction, phnD, upgA and upgC in P transportation and phnI, phnK, phoA and opd in microbial organic P mineralization, were all closely linked to U geochemical distribution, species and cycling. All these findings disclose the functional genes that may control the transfer and transformation behavior of U in soil environment, which provides important and novel indications for the bio-remediation strategies towards U polluted sites.

Integrating land-sea coordination into construction of an ecological security pattern for urban agglomeration: a case study in the Guangdong-Hong Kong-Macao Greater Bay Area

The construction of ecological security pattern (ESP) is of great scientific significance for solving the problem of habitat fragmentation in urban environment. However, previous studies mainly focused on the ESP in land area, leaving the sea area to be ignored. This study took the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) and its offshore area as an example and integrated the land-sea coordination into the construction of ESP based on the minimum resistance model, gravity model, and graph theory centrality. The results showed that there are 171 and 56 ecological sources for land area and offshore area, accounting for 31.46% and 21.51% of total area, respectively. Twenty-four important ecological corridors with a total length of 2738.05 km were identified in GBA, and the width is proposed to be less than 100 m. Moreover, the α, β, and γ index of the ecological network in the study area is 0.19, 1.33, and 0.5, respectively, indicating that the ecological network structure is complex and the connectivity between ecological nodes is good. The ecological restoration area includes 286.6 km2 of ecological pinch points and 140.44 km2 of ecological barrier. The overall ESP of the study area is "one ring, two belts, and four zones." The main body of the area with a superior ecological environment is distributed in a ring-like pattern near the outer edge of the study area, and two belts (important ecological corridor and ecological corridor) are distributed in a network. According to the ecological characteristics, the study area was divided into four zones: ecological preservation areas, ecological restoration areas, limited construction areas, and optimized construction areas. The ESP established herein institute provides a reference for the revision of ecological space control and optimization measures in the GBA. It also provides effective and systematic means to solve ecological problems in the current territorial spatial planning and territorial ecological restoration of coastal urban agglomeration.

Identifying and optimizing ecological spatial patterns based on the bird distribution in the Yellow River Basin, China

In the Yellow River Basin (YRB), there exists a rich biodiversity of species that has been shaped by its unique geography, climate, and human activities. However, the high speed of economic development has resulted in the fragmentation and loss of habitats that are crucial for the survival of these species. To address this problem, constructing ecological networks has emerged as a promising approach for biodiversity preservation. In the study, we centered on the YRB and employed bird communities as an indicator species to identify ecological sources by combining bioclimatic variables and land use data with the Maximum Entropy (MaxEnt) and Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) models. We generated a resistance surface using various data such as Digital Elevation Model (DEM), the Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), nighttime light, road density, railway density, and waterway density. So, we then simulated ecological corridors applying the Minimum Cumulative Resistance (MCR) model and constructed a bird diversity protection network. The results we found suggested that bird hotspots were predominantly clustered upstream and downstream in the YRB. We identified 475 sources covering a total area of 65,088 km2, 681 corridors with a total length of 11,495.05 km. This network served as a critical ecological facility to sustain and protect biodiversity. The bird ecological corridors in the YRB showed that a dense east-west pattern in the central area, with a short length in the west and east and a long length in the central area. Although the central region lacked ecological sources, the east and west were still connected as a tight whole. Two scenarios showed adding ecological stepping stones had a better optimization effect than enhancing ecological connectivity.

A coral-associated actinobacterium mitigates coral bleaching under heat stress

BACKGROUND

The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora damicornis with capabilities to synthesize antioxidants, vitamins, and antibacterial and antiviral compounds supported with phenotypic and/or genomic evidence. Strain SCSIO 13291 was labeled with 5 (and - 6)-carboxytetramethylrhodamine, succinimidyl ester and the labeled cell suspension directly inoculated onto the coral polyp tissues when nubbins were under thermal stress in a mesocosm experiment. We then visualized the labelled bacterial cells and analyzed the coral physiological, transcriptome and microbiome to elucidate the effect this strain conferred on the coral holobiont under thermal stress.

RESULTS

Subsequent microscopic observations confirmed the presence of the bacterium attached to the coral polyps. Addition of the SCSIO 13291 strain reduced signs of bleaching in the corals subjected to heat stress. At the same time, alterations in gene expression, which were involved in reactive oxygen species and light damage mitigation, attenuated apoptosis and exocytosis in addition to metabolite utilization, were observed in the coral host and Symbiodiniaceae populations. In addition, the coral associated bacterial community altered with a more stable ecological network for samples inoculated with the bacterial strain.

CONCLUSIONS

Our results provide insights into the benefits of a putative actinobacterial probiotic strain that mitigate coral bleaching signs. This study suggests that the inoculation of bacteria can potentially directly benefit the coral holobiont through conferring metabolic activities or through indirect mechanisms of suppling additional nutrient sources.

Natural restoration exhibits better soil bacterial network complexity and stability than artificial restoration on the Loess Plateau, China

Natural restoration (NR, e.g., secondary succession) and artificial restoration (AR, e.g., afforestation) are key approaches for rehabilitating degraded land; however, a comparative assessment of microbial network between these approaches is lacking. We compared bacterial networks under NR and AR in two different watersheds on the Loess Plateau. Our findings revealed significantly heightened network complexity under NR compared to AR, including metrics such as node, edge, modularity, degree, centrality, and keystone nodes. NR's network robustness exceeded AR by 19.45-35.9% and 7.79-17.74% in the two watersheds, aligning with the ecological principle that complexity begets stability. The significantly higher negative/positive cohesion and natural connectivity under NR also support its better network stability than AR. Integrated analysis of paired sequencing data from five Loess Plateau studies conducted on the Loess Plateau further confirmed the higher complexity and stability of bacterial networks under NR. Further analysis unveiled "biological interactions" as primary drivers of bacterial co-occurrence (on average 84.21% of links), surpassing the influence of environmental filtering (5.17%) or dispersal limitation (4.2%). Importantly, networked communities under NR exhibited generally stronger linkages with various ecosystem function than AR. Overall, our study provides insights into vegetation restoration strategies from the perspective of microbial network, underscoring natural regeneration's potential as a superior remedy for degraded-land restoration.

Effects of flow velocity on biofilm composition and microbial molecular ecological network in reclaimed water distribution systems

The existence of biofilm on the reclaimed water pipeline seriously affects the safety of water distribution. And the flow regimes in the pipeline play a crucial role in the growth of biofilms. In this study, the biofilm composition, surface topography and bacterial community were detected under eight levels of flow velocity in the range of 0.10-1.40 m s-1. The results showed that the dry weight, the concentration of extracellular protein and extracellular polysaccharide in the biofilm reached a dynamic stable period after 640 h. The biofilm composition and surface topography of biofilm were significantly different under the different flow regimes (laminar flow belongs to [0.10, 0.19] m s-1, and turbulent flow belongs to [0.29, 1.40] m s-1). As the flow velocity range increases, the concentration of each component in the biofilm and the parameters of biofilm surface topography increased and then decreased. The flow velocity could be a strong environmental stimulus resulting in the succession of bacterial community in biofilm. As the flow velocity increased from 0.10 m s-1 to 1.40 m s-1, at the phylum level, the average relative abundance of Firmicutes mainly showed a trend of first increasing and then decreasing with the highest abundance value of 71.57% at 0.49 m s-1. The flow velocity increased from 0.10 m s-1 to 0.49 m s-1, a significant increase in microbial diversity could be detected. The increase in flow velocity promoted the proliferation of microorganisms, and the interaction between different microbial components was enhanced. At 0.49 m s-1, the function of the biofilm is complex, and the ability to resist environmental stress is the strongest. This study can effectively improve the cognition depth of biofilms under the influence of flow velocity in the reclaimed water distribution systems, and provide an important theoretical support for the safe distribution of reclaimed water.

The role of the core microorganisms in the microbial interactions in activated sludge

In order to gain a deeper understanding of the microbial interactions in wastewater treatment plants (WWTPs) in China and clarify the role of the core community in the microbial interactions in activated sludge (AS), this study used a molecular ecological network approach based on random matrix theory to construct co-occurrence networks of the core microorganisms (CoreN), the whole AS community (WholeN) and the microbial communities without the core microorganisms (OtherN), respectively. It was shown that the WholeN had more complex and tighter connections compared with the OtherN, because of its higher total number of nodes, higher average clustering coefficient, and shorter average geodesic distance. The proportions of positive links in the CoreN, WholeN and OtherN were gradually decreased, indicating that the core microorganisms promoted cooperation between AS microorganisms. Moreover, higher robustness after random removal of 50% of the nodes of the WholeN (0.2836 ± 0.0311) was observed than the robustness of the OtherN (0.1152 ± 0.0263). In addition, the vulnerability of OtherN (0.0514) is significantly higher than WholeN (0.0225). Meanwhile, the average ratio of negative/positive cohesion, was significantly decreased when the core microorganisms were removed. These results demonstrated that core community could strengthen the stability of the ecological network in AS. By discerning the key factors affecting ecological network, AS temperature was observed to have a strong correlation with all three networks. Moreover, pollutants in wastewater shown stronger correlations with the CoreN and WholeN, supporting the point that core community play a critical role in pollutant removal in WWTPs to a certain extent.

Spatiotemporal ecosystem services: Response to structural changes (A case study in Lahijan, Iran)

Structure and function are the inherent characteristics of each ecosystem providing various services such as clean air, extreme weather mitigation, and mental and physical well-being. The objective of this study is to develop a unified model combining Integrated Valuation of Ecosystem Services, ecological network (EN), and correlation analysis to investigate changes in ecosystem structure, function, and process. In this context, carbon sequestration, soil reduction, and flood risk mitigation were quantified from 2000 to 2020 and predicted for 2040 using the cellular automata and Markov chain (CA-Markov) model. Finally, correlation analysis was used to analyze the relationship over time between the land use (LU) classes and the components of the forest EN that provide and exchange desired ecosystem services (ESs). Thus, the changes in LU in the region in recent years led to significant reduction of ESs in the region as well as changes in the interaction between services. These changes, on the one hand, reduced the area of cores and increased isolated forest patches and, on the other hand, led to the horizontal expansion of cities and agricultural lands. If this trend continues, the decline in services provided by the ecosystem will persist into the future. Consequently, it can be said that structural changes in the ecosystem can lead to changes in the ESs. Integr Environ Assess Manag 2023;00:1-13. © 2023 SETAC.

Untangling microbiota diversity and assembly patterns in the world's longest underground culvert water diversion canal

The long-distance underground box culvert water transport system (LUBWT) is a crucial link between the source of drinking water and the consumers. It must ensure the stability of water quality during transportation. However, uncontrollable microbial growth can develop in the water delivery system during the long delivery process, posing a risk to health and safety. Therefore, we applied 16 s and 18 s gene sequence analysis in order to study microbial communities in box culvert waters sampled in 2021, as well as a molecular ecological network-based approach to decipher microbial interactions and stability. Our findings revealed that, in contrast to natural freshwater ecosystems, micro-eukaryotes in LUBWT have complex interactions such as predation, parasitism, and symbiosis due to their semi-enclosed box culvert environment. Total nitrogen may be the primary factor affecting bacterial community interactions in addition to temperature. Moreover, employing stability indicators such as robustness and vulnerability, we also found that microbial stability varied significantly from season to season, with summer having the higher stability of microbial communities. Not only that but also the stability of the micronuclei also varied greatly during water transport, which might also be related to the complex interactions among the micro-eukaryotes. To summarize, our study reveals the microbial interactions and stability in LUBWT, providing essential ecological knowledge to ensure the safety of LUBWT's water quality.

Wastewater treatment plant effluent discharge decreases bacterial community diversity and network complexity in urbanized coastal sediment

The wastewater treatment plant (WWTP) effluent discharge affects the microorganisms in the receiving water bodies. Despite the ecological significance of microbial communities in pollutant degradation and element cycling, how the community diversity is affected by effluent remains obscure. Here, we compared the sediment bacterial communities exposed to different intensities of WWTP effluent discharge in Hangzhou Bay, China: i) a severely polluted area that receives effluent from an industrial WWTP, ii) a moderately polluted area that receives effluent from a municipal WWTP, and iii) less affected area that inner the bay. We found that the sediment bacterial diversity decreased dramatically with pollution levels of inorganic nutrients, heavy metals, and organic halogens. Microbial community assembly model analysis revealed increased environmental selection and decreased species migration rate in the severely polluted area, resulting in high phylogenetic clustering of the bacterial communities. The ecological networks were less complex in the two WWTP effluent receiving areas than in the inner bay area, as suggested by the smaller network size and lower modularity. Fewer negative network associations were detected in the severely (6.7%) and moderately (8.3%) polluted areas than in the less affected area (16.7%), indicating more collaborative inter-species behaviors are required under stressful environmental conditions. Overall, our results reveal the fundamental impacts of WWTP effluents on the ecological processes shaping coastal microbial communities and point to the potential adverse effects of diversity loss on ecosystem functions.

Improving the ecological network optimization with landscape connectivity: a case study of Neijiang City, Sichuan Province

Rapid urbanization intensifies the fragmentation of landscape patches and affects the stability of ecosystems. The construction of an ecological network can effectively promote the connection of important ecological spaces and improve the landscape integrity. However, the landscape connectivity, directly affecting the stability of ecological network, was less considered in the ecological network construction of recent researches, which easily caused the instability of constructed ecological network. Therefore, this study introduced landscape connectivity index to establish a modified ecological network optimization method based on the minimum cumulative resistance (MCR) model. The results showed that, compared with the traditional model, the modified model focused on the spatially detailed measurement of regional connectivity, and emphasized the impact of human disturbance on ecosystem stability at the landscape scale. The constructed corridors in the optimized ecological network of the modified model not only effectively improved the connection degree between important ecological sources but also avoided the areas with low landscape connectivity and high obstacles to ecological flow, especially in the counties of Zizhong, Dongxing, and Longchang within the focal study area. The ecological network established by the traditional model and modified model generated 19 and 20 ecological corridors with lengths of 334.49 km and 364.35 km, respectively, and the number of ecological nodes was 18 and 22. Evaluated by the Gravity method, the modified model identified the important ecological corridors in the ecological network, and the energy transfer efficiency of the network was improved. This study provided an effective way to improve the structural stability of ecological network construction and can provide scientific support for regional landscape pattern optimization and ecological security construction.

Depth-dependent patterns of soil microbial community in the E-waste dismantling area

The long-term dismantling of electronic waste (E-waste) has contaminated the soil environment considerably. In spite of this, it is unknown if it affects the depth-resolved microbial communities. In the present research, six soil profiles (dismantling sites and the surrounding farmland) were collected from one of the largest Chinese E-waste disposal centers to identify depth-resolved microbiota and assess how heavy metal contamination affects microbial adaptation. Results suggested that cadmium (0.12-7.22 mg kg^-1) and copper (18.99-11282.03 mg kg^-1) were the main pollutants in the test soil profiles, and their concentrations gradually decreased with depth. The surrounding contaminated farmland has a more complex interaction and higher modularity (0.77-0.85) among microbes, indicating a stronger niche differentiation to enhance functional diversity. The proportion of positive interactions between taxa decreased with depth, as high heavy metals contamination in the topsoil results in the co-occurrence of microorganisms with the same ecological niche that collaborated to face environmental stress. Soil physicochemical properties, heavy metals concentration, and soil depth critically affect microbial communities. Microbial community assembly processes in the topsoil were affected by environmental filtering, i.e., by deterministic processes (NST: 13-52%), while were more stochastic (NST: 46-72%) in the subsoil due to the environment of soil becoming more homogeneous as soil depth increased.

Freshwater species diversity loss embodied in interprovincial hydroelectricity transmission with ecological network analysis

A major strategy for addressing the imbalance in source-network-load distribution is interprovincial electricity transmission; however, this process also causes various environmental effects. Previous studies have mainly examined thermal power transmission, and few insights have been gained into the challenges hydroelectricity transmission poses for biodiversity conservation. Here, we innovatively incorporated the freshwater species diversity footprint into a hydropower environmental impact assessment, calculating the interprovincial transfer of freshwater species diversity embodied in hydroelectricity transmission. We proposed an evaluation model of an interprovincial hydroelectricity transmission network using freshwater species diversity as the ecological element and creatively identified significant nodes and paths of the network. Up to 28% of the transfer of freshwater species diversity was related to the demand for hydroelectricity consumption in Shanghai. 64% of the relationships in the hydroelectricity transmission network were implemented at the expense of ecological losses on one side. Shanghai and Sichuan provinces and some transmission lines related to them were significant nodes and paths for improving the overall status of the network. This research can help policymakers comprehend the challenges to freshwater species presented by interprovincial hydroelectricity transmission and serve as a reference for ecological compensation for hydropower development.

Simultaneous methanogenesis and denitrification coupled with nitrifying biofilm for high-strength wastewater treatment: Performance and microbial mechanisms

A combined system consisting of an upflow blanket filter (UBF) and a moving-bed biofilm reactor (MBBR) was developed for the simultaneous removal of organic matters and ammonia from high-strength wastewater. With a constant COD of approximately 2000 mg/L and ammonium nitrogen in a series of concentrations (e.g., 50, 200 and 400 mg/L in stages I to III) of the influent wastewater, the removal efficiencies of COD, ammonium nitrogen and total nitrogen reached 96.10%-98.19%, 100%, and 79.12%-82.15%, respectively. With the increase of influent ammonia nitrogen concentration, the specific methanogenic activity of the UBF granules decreased significantly, while the specific denitrification rates of the UBF granules and specific nitrification rates of the MBBR biofilms increased significantly. Microbial community analysis showed that Methanobacterium and Methanosaeta were the dominant methanogens in the UBF granules, while Candidatus Competibacter, Thauera and Acinetobacter were identified as dominant denitrifiers. In addition, nitrifiers were enriched in MBBR biofilms at 11.33% and 13.87% of the average abundance of Nitrosomonas and Nitrospira, respectively, at stage III (influent ammonium at 400 mg/L, COD/NH₄⁺-N =  5). The ecological network analysis, including full-networks and sub-networks, indicated that the interactions between methanogens and denitrifiers in the UBF granules were strong when the influent ammonium concentration reached 400 mg/L. No intensive interactions were observed among the functional bacteria in the MBBR biofilms over the entire operation. Overall, this study provides a new strategy for the application and construction of efficient biological processes to achieve simultaneous removal of organic matter and nitrogen for high-strength wastewater treatment.

Integrating circuit theory and landscape pattern index to identify and optimize ecological networks: a case study of the Sichuan Basin, China

The notion of ecological networks (EN) and their identification can support approaches to nature conservation strategies aiming at biodiversity, landscape connectivity, and people's well-being. Integrating ecosystem services (ESs), morphological spatial pattern analysis (MSPA), circuit theory, and landscape pattern index analysis, we proposed a new framework for mapping EN that was expected to promote economic development and ecological protection. Specifically, source areas were extracted through a combination of ESs and MSPA that integrated functional and morphological spatial attributes. Resistance surfaces were determined based on habitat quality. A network linking ecological source areas was then identified using circuit theory, and landscape pattern index analysis was used to identify ecological strategy nodes in view of the heterogeneity within ecological corridors. The results showed that the Sichuan Basin involved 553 ecological sources, 641 ecological corridors, and 33 ecological nodes that altogether included 20 ecological strategy nodes. Constructing regional EN can promote the transformation of multiple, chaotic, and scattered ecological elements to systematic and networked ecological elements and ultimately promote harmonious coexistence between humans and nature. This study provided a methodology for the extraction of ecological source areas and strategy nodes and can provide a significant reference for the management and optimization of EN.

Stability-instability transition in tripartite merged ecological networks

Although ecological networks are typically constructed based on a single type of interaction, e.g. trophic interactions in a food web, a more complete picture of ecosystem composition and functioning arises from merging networks of multiple interaction types. In this work, we consider tripartite networks constructed by merging two bipartite networks, one mutualistic and one antagonistic. Taking the interactions within each sub-network to be distributed randomly, we consider the stability of the dynamics of the network based on the spectrum of its community matrix. In the asymptotic limit of a large number of species, we show that the spectrum undergoes an eigenvalue phase transition, which leads to an abrupt destabilisation of the network as the ratio of mutualists to antagonists is increased. We also derive results that show how this transition is manifest in networks of finite size, as well as when disorder is introduced in the segregation of the two interaction types. Our random-matrix results will serve as a baseline for understanding the behaviour of merged networks with more realistic structures and/or more detailed dynamics.

Spatiotemporal pattern of specialization of sunbird-plant networks on Mt. Cameroon

Differences in interaction specializations between nectarivorous birds and plants across continents serve as common examples of evolutionary trajectory specificity. While New World hummingbird-plant networks have been extensively studied and are considered highly specialized, knowledge on the network specialization of their Old World counterparts, sunbirds (Nectariniidae), remains limited. A few studies from tropical Africa indicate that sunbird-plant networks are rather generalized. Unfortunately, these studies are limited to dry seasons and high elevations at the tree line, environments where niche-based hypotheses also often predict lower resource partitioning. In our study, we explored the specialization of sunbird-plant networks and their spatiotemporal variability on Mt. Cameroon (Cameroon). Using a combination of automatic video recordings and personal observations, we constructed eight comprehensive sunbird-plant networks in four forest types at different elevations in both the dry and wet seasons. As reported in previous studies, the montane forest plants, birds and whole networks were highly generalized. Nevertheless, we observed a much higher specialization in forests at lower elevations. Except at the lowest altitude, the wet season was also characterized by higher specialization. While less specialized flowering trees dominated in the dry season networks, more specialized herbs and shrubs were visited by birds during the wet season. As our findings do not support the generally accepted assumption that Old World bird-plant networks are rather generalized, we need further studies to understand the differences in bird-plant specializations on individual continents.

Comparing biotransformation of extracellular polymeric substances (EPS) under aerobic and anoxic conditions: Reactivities, components, and bacterial responses

This study aimed to better understand the transformation behaviors of extracellular polymeric substances (EPS) and their roles in regulating bacterial community in biological wastewater treatment processes. Herein, well-controlled bioassays under aerobic and anoxic conditions were performed to investigate degradation dynamics, composition variations, and bacterial response during EPS transformation. Reactivity continuum modeling showed that organic pools of EPS had continuous reactivity distributions, and most labile organic fraction with a degrading rate >0.1 h^-1 was substantially higher under aerobic (20.47%) than anoxic (2.02%) condition. Rapid degradation of protein-like substances in the initial degradation stage was accompanied by the humification process, as revealed by UV absorption spectroscopy, fluorescence spectroscopy, and size exclusion chromatography with continuous organic carbon detection analysis. The 16S rRNA gene sequencing results showed that the selection effect of EPS in controlling abundant populations during their transformation, e.g., Acinetobacter was enriched, and Candidatus Competibacter was washed out relative to the source community. Furthermore, taxonomic normalized stochasticity ratio-based null model and bacterial ecological network analysis indicated higher relative importance of deterministic process in shaping the EPS-degrading communities under aerobic than anoxic condition, likely explaining the faster EPS biotransformation under aerobic condition. Intriguingly, the keystone populations driving EPS metabolism showed the environmental filtering characteristics (e.g., capable of degrading refractory and aromatic compounds or adapting to harsh environments) and cooperative interactions with the co-occurring species under both conditions. This work is expected to reveal the fates and roles of EPS in wastewater treatment plants extensively.

Comparative ecological network pattern analysis: a case of Nanchang

Urban-ecological landscape connectivity and pattern optimization can significantly enhance biodiversity and sustainable development capacity, which play an important role in continued ecosystem functioning. Previous studies identified ecological sources based on the area threshold method or combination with morphological spatial pattern analysis and the landscape connectivity index (CMSPACI) method, but few studies have compared the advantages, disadvantages, and applicability of the two methods. In this paper, taking Nanchang as the study area, we address the ecological sources via area threshold and the CMSPACI method. Then, the minimum cost distance method is used to generate potential corridors of different methods, and the differences in ecological networks are analyzed. Finally, the circuit theory is used to identify barriers, and we provide targeted recommendations for ecological network pattern optimization in the study area. The results show that (1) the ecological sources extracted by different methods are different. The ecological sources extracted by the area threshold are far away from the surrounding sources, and the landscape connectivity is low. The ecological sources identified by the CMSPACI method are closely related to the surrounding sources, and the landscape connectivity is high. (2) Compared with the area threshold method, the habitat quality of corridors under the CMSPACI method is better, and the interaction intensity between patches is larger. (3) There is little difference in the number of ecological barriers under different methods; all of them are located between patches or on the edge of patches, and most of them are roads or construction land. Overall, the area threshold method is simpler. Ecological sources can be effectively addressed through the CMSPACI method, and the landscape connectivity of the ecological network will be better. This study provides an important reference for the selection of ecological sources in the construction of ecological networks.

Fungal communities in feces of the frugivorous bat Ectophylla alba and its highly specialized Ficus colubrinae diet

BACKGROUND

Bats are important long-distance dispersers of many tropical plants, yet, by consuming fruits, they may disperse not only the plant's seeds, but also the mycobiota within those fruits. We characterized the culture-dependent and independent fungal communities in fruits of Ficus colubrinae and feces of Ectophylla alba to determine if passage through the digestive tract of bats affected the total mycobiota.

RESULTS

Using presence/absence and normalized abundance data from fruits and feces, we demonstrate that the fungal communities were significantly different, even though there was an overlap of ca. 38% of Amplicon Sequence Variants (ASVs). We show that some of the fungi from fruits were also present and grew from fecal samples. Fecal fungal communities were dominated by Agaricomycetes, followed by Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Malasseziomycetes, while fruit samples were dominated by Dothideomycetes, followed by Sordariomycetes, Agaricomycetes, Eurotiomycetes, and Laboulbeniomycetes. Linear discriminant analyses (LDA) show that, for bat feces, the indicator taxa include Basidiomycota (i.e., Agaricomycetes: Polyporales and Agaricales), and the ascomycetous class Eurotiomycetes (i.e., Eurotiales, Aspergillaceae). For fruits, indicator taxa are in the Ascomycota (i.e., Dothideomycetes: Botryosphaeriales; Laboulbeniomycetes: Pyxidiophorales; and Sordariomycetes: Glomerellales). In our study, the differences in fungal species composition between the two communities (fruits vs. feces) reflected on the changes in the functional diversity. For example, the core community in bat feces is constituted by saprobes and animal commensals, while that of fruits is composed mostly of phytopathogens and arthropod-associated fungi.

CONCLUSIONS

Our study provides the groundwork to continue disentangling the direct and indirect symbiotic relationships in an ecological network that has not received enough attention: fungi-plants-bats. Findings also suggest that the role of frugivores in plant-animal mutualistic networks may extend beyond seed dispersal: they may also promote the dispersal of potentially beneficial microbial symbionts while, for example, hindering those that can cause plant disease.

Microbial response and adaption to thallium contamination in soil profiles

Thallium (Tl) is a trace metal with high toxicity. Comprehensive investigation of spatial distribution of Tl and microorganism is still limited in soils from mining area. In this study, 16S rRNA sequencing and network analysis were used for deciphering the co-occurrence patterns of bacterial communities in two different types of soil profiles around a typical Tl-bearing pyrite mine. The results showed that geochemical parameters (such as pH, S, Tl, Fe and TOM) were the driving forces for shaping the vertical distribution of microbial community. According to network analysis, a wide diversity of microbial modules were present in both soil profiles and affected by depth, significantly associated with variations in Tl geochemical fractionation. Phylogenetic information further unveiled that the microbial modules were mainly dominated by Fe reducing bacteria (FeRB), Fe oxidizing bacteria (FeOB), S oxidizing bacteria and Mn reducing bacteria. The results of metagenome indicated that Fe, Mn and S cycle in soil are closely involved in the biogeochemical cycle of Tl. The findings of co-occurrence patterns in the bacterial network and correlation between microorganisms and different geochemical fractions of Tl may benefit the strategy of bioremediation of Tl-contaminated soils with indigenous microbes.

Effect of sludge retention time on microbial succession and assembly in thermal hydrolysis pretreated sludge digesters: Deterministic versus stochastic processes

Thermal hydrolysis process (THP) assisted anaerobic digestion (AD) has been demonstrated to be an efficient approach to improve biogas production and solids reduction. Given the faster reaction kinetics in the THP-AD system, reduction of sludge retention time (SRT) is possible. However, a comprehensive understanding of the effects of sludge retention time (SRT) on microbial dynamics and community assemblages is still lacking in THP-AD systems. Thus, twelve THP-AD reactors were operated at different SRTs (10-30 d) to fulfill the knowledge gap. Results showed that, although all the bioreactors displayed good performance, shorter SRT reactors (SRT 10 d) took a longer time to reach the stable state. The total biogas production at SRT of 10 d was lower than that at other longer SRTs, attributing to the limited hydrolytic/fermentative capacities of AD microbiomes. Different SRTs resulted in distinct succession patterns of AD microbiomes. THP sludge reduced the microbial diversity in all the bioreactors over time, but longer SRTs maintained higher biodiversity. Null model analysis suggested that THP-AD microbial community assembly was predominately driven by deterministic selection at the tested SRT range, but stochasticity increased with elevated SRTs, likely attributing to the immigrants from the feedstock. Phylogenetic molecular ecological networks (pMENs) analysis revealed more stable network structures at longer SRTs, evidenced by the lower modularity, shorter harmonic geodesic distance, and higher connectivity. The potential keystone taxa under varied SRTs were identified, some of which were hydrolytic/fermentative bacteria (e.g., Peptostreptococcus, Lutispora, Synergistaceae), suggesting that these species related to organic hydrolysis/fermentation even with low-abundance could still play pivotal ecological roles in maintaining the THP-AD microbial community structure and functions. Collectively, this study provides comprehensive and in-depth insights into the mechanisms underlying community assembly in THP-AD reactors, which could aid in diagnosing system stability.

Bottom-up cascading effects of quarry revegetation deplete bird-mediated seed dispersal services

Quarrying activities cause profound modifications on ecosystems, such as removal of vegetation cover, biodiversity loss and depletion of ecosystem services. Ecological restoration stands as a solution to revert such effects. Concomitantly, awareness is currently being given on ecosystem services and ecological processes to evaluate restoration efficiency. The objective of the study was to assess restoration success in a quarry subjected to restoration practices for the last 40 years involving the plantation of native Mediterranean vegetation and the non-native Aleppo pine Pinus halepensis. The study was carried out by assessing the effectiveness of seed dispersal service provided by birds in the restored quarry by comparing this service to neighbouring natural (shrubland) and other semi-natural areas (oak-pine mixed open and Aleppo pine forest) present at the landscape. For this purpose, we explored bird composition structure and seed dispersal networks using point counts and faecal samples of mist-netted birds. We also collected vegetation structure data and explored its effect on bird community composition. Our results showed that bird abundance in the restored quarry was significantly lower, and its bird community was compositionally different than natural shrubland and semi-natural areas. For instance, seed-dispersing birds, woody and shrub/ground foragers and partially migrators were the most affected groups at the restored area. Bird community composition and their traits were likely driven by vegetation characteristics, with higher native vegetation cover and fruit richness promoting higher bird abundance and Aleppo pine cover negatively influencing seed-dispersing birds. Concurrently, seed dispersal network in the restored quarry was less complex than in other areas. Seed dispersal services in the restored quarry were below the reported values for neighbouring natural and semi-natural areas and are likely driven by the low abundance of seed-dispersing birds. We consider that the causes affecting this group's low abundance can be related to revegetation measures favouring Aleppo pine, combined with a shallow soil depth and poor soil quality, which may have constrained native vegetation development. We conclude that seed dispersal services at the quarry are depleted, which may suggest a low restoration success concerning ecosystem functioning. Our results strengthen that quarry revegetation with non-native species must be avoided, since it alters bird community composition, and consequently, affects seed dispersal service provided by birds.

Spartina alterniflora invasions reduce soil fungal diversity and simplify co-occurrence networks in a salt marsh ecosystem

Soil fungal communities drive diverse ecological processes and are critical in maintaining ecosystems' stability, but the effects of plant invasion on soil fungal diversity, community composition, and functional groups are not well understood. Here, we investigated soil fungal communities in a salt marsh ecosystem with both native (Suaeda salsa) and exotic (Spartina alterniflora) species in the Yellow River Delta. We characterized fungal diversity based on the PCR-amplified Internal Transcribed Spacer 2 (ITS2) DNA sequences from soil extracted total DNA. The plant invasion evidently decreased fungal richness and phylogenetic diversity and significantly altered the taxonomic community composition (indicated by the permutation test, P < 0.001). Co-occurrence networks between fungal species showed fewer network links but were more assembled because of the high modularity after the invasion. As indicated by the fungal Bray-Curtis and weighted UniFrac distances, the fungal community became homogenized with the invasion. FUNGuild database analyses revealed that the invaded sites had a higher proportion of saprophytic fungi, suggesting higher organic matter decomposition potential with the invasion. The plant invasion dramatically inhibited the growth of pathogenic fungi, which may facilitate the expansion of invasive plants in the intertidal habitats. Soil pH and salinity were identified as the most important edaphic factors in shaping the fungal community structures in the context of Spartina alterniflora invasion. Overall, this study elucidates the linkage between plant invasion and soil fungal communities and poses potential consequences for fungal contribution to ecosystem function, including the decomposition of soil organic substrates.

Spatial influence of ecological networks on land use intensity

Rapid urbanization resulted in widespread urban expansion and the fragmentation and isolation of large-scale ecological sources. Ecological sustainability has propelled the popularity and implementation of intensive land use programs worldwide, in China particularly. In this study, we explored the spatial spillover effect through ecological networks on intensive urban land use and the underlying driving mechanism using the Wuhan urban agglomeration as the case study area. First, we comprehensively measured land use intensity (LUI) from three dimensions: input, output, and landscape aggregation. Second, ecological sources were identified on the basis of land use maps, and ecological networks were constructed using the "minimum cumulative resistance" model. Then, the "gravity model" was applied to measure the spatial interaction among ecological sources and to construct spatial weight matrices for spatial modeling. Lastly, we devised a spatial Durbin model using the designed "ecological" spatial weight matrices to examine the influencing factors and the potential spatial interactions or constraints. The results showed that the average values of LUI in 2017 were almost 70 times higher than that in 2005 and the Jianghan District had the highest increment (91 times) from 2005 to 2017. LUI was primarily driven by socioeconomic development. Gross domestic product and proportion of tertiary sector exerted positive influences, whereas agricultural output value exhibited a negative effect on LUI in 2005 and 2017. A positive spatial autocorrelation of LUI was observed at the county level, and the spatial spillover effect was confirmed through ecological networks during intensive land use, indicating that ecological spatial influence is an important factor in explaining LUI. The findings help in exploring the spatial influence through ecological networks on LUI at the regional level and provide references for formulating relevant policies to achieve the ecological security of terrestrial ecosystems and coordinated and balanced regional sustainable development.

Evaluation of River Fragmentation and Implications for the Conservation of Migratory Fish in Southeastern Brazil

In freshwater systems, the abundance and diversity of long-distance migratory fish are limited by the maintenance of longitudinal connectivity and natural flow regimes of rivers. Using a graph-based view of each riverscape, we analyzed the river fragmentation process and overlapped with the probable number of migratory species in each remaining stretch. Applying this methodology in basins, we assess historical and potential scenarios quantifying segment extensions free from dams determining the fish richness based on the available habitat for each species. The highest number of migratory species was observed in fragments longer than 100 km. In the future scenario, there was an increase in the number of fragments, with an increase in the number of stretches shorter than 50 km, inadequate to maintain most of the migratory species. Segments of the highest classification order and located in the longest lotic fragments were considered the most important for the species habitat conservation. Dam construction in these segments could seriously affect the ecological processes at a regional level. The proposed analyses enable to approach basins with high diversity of species and nonsalmonid species, supporting the lack of base data concerning those areas, and determine priorities for studies and conservation.

Large-sized planktonic bioaggregates possess high biofilm formation potentials: Bacterial succession and assembly in the biofilm metacommunity

Wanted and unwanted surface-attached growth of bacteria is ubiquitous in natural and engineered settings. Normally, attachment of planktonic cells to media surfaces initiates biofilm formation and fundamentally regulates biofilm assembly processes. Here, culturing biofilm with planktonic sludge as source community, we found distinct succession profiles of biofilm communities sourced from the size-fractionated sludge flocs (<25; 25-120; >120 μm). Null model analyses revealed that deterministic process dominated in biofilm community assemblies but decreased with decreasing floc size. Additionally, the relative importance of environmental selection increased with increasing floc size of the source sludge, whereas homogenizing dispersal and ecological drift followed opposite trends. Phylogenetic molecular ecological networks (pMENs) indicated that species interactions were intensive in biofilm microbiota developed from large-sized flocs (>120 μm), as evidenced by the low modularity and harmonic geodesic distance and the high average degree. Intriguingly, the keystone taxa in these biofilm ecological networks were controlled by distinct interaction patterns but all showed strong habitat characteristics (e.g., facultative anaerobic, motile, hydrophobic and involved in extracellular polymeric substance metabolism), corroborating the crucial roles of environmental filtering in structuring biofilm community. Taken together, our findings highlight the role of planktonic floc properties in biofilm community assembly and advance our understanding of microbial ecology in biofilm-based systems.

Temperature mainly determines the temporal succession of the photosynthetic picoeukaryote community in Lake Chaohu, a highly eutrophic shallow lake

Photosynthetic picoeukaryotes (PPEs) are key players in aquatic systems, while their diversity and community composition dynamics remain poorly understood. The monthly composition of PPEs in Lake Chaohu was investigated using a combination of flow cytometry sorting and high throughput sequencing. Results indicated that temperature is the most important factor shaping PPEs community structure. The PPEs community can be categorized into three groups that are dominant at different temperature ranges: high temperature (>21.8 °C), intermediate temperature (between 9.8 °C and 21.8 °C) and low temperature (<9.8 °C). At the supergroup level, Cryptophyta were dominant at the intermediate temperature level, and Bacillariophyta were prevalent at low temperatures. In comparison, Chlorophyta PPEs were sensitive to temperature at the order level. Molecular network analysis using 18S rDNA sequencing results from sorted samples revealed that the Operational Taxonomic Units (OTUs) of PPE from the same taxonomic groups were predominantly positive, implying that they were occupying similar niches. The cooccurrence patterns between PPEs and fungi were mostly negative. In particular, OTU101, which was associated with Chytridiomycota, was negatively related to many OTUs belonging to Chlorophyta and Diatom, indicating that their potential parasitic associations may be not species-specific.

Co-occurrence patterns of microbial communities affected by inoculants of plant growth-promoting bacteria during phytoremediation of heavy metal-contaminated soils

Phytoremediation assisted by plant growth-promoting bacteria (PGPB) is an alternative method of cleaning up toxic metals from soil. However, the interactions among indigenous soil microorganisms following PGPB inoculation are far from fully understood, although these interactions are conducive to evaluate the effectiveness of PGPB. Here, we used Illumina Miseq sequencing and network analysis to decipher the co-occurrence patterns of bacterial communities following PGPB inoculation during phytoremediation of heavy metal contaminated soil. Miseq sequencing revealed that PGPB inoculation changed the bacterial community composition one day after inoculation, with minor changes continuing to be observed ten days after inoculation. This suggested that PGPB inoculants did not proliferate extensively in a new environment. Network analysis showed that PGPB inoculation altered the co-occurrence patterns, dominant modules and topological roles of individual OTUs. In the presence of PGPB inoculants the bacterial community had more complex and compact associations. Moreover, PGPB inoculation increased the percentage of connectors, indicating that PGPB may contribute to more intensified interactions among OTUs from different modules; consequently, the microbial community would be more ordered and efficient. The enhanced co-occurrence associations in the PGPB-inoculated bacterial network may contribute to the plant growth-promoting effects of PGPB during phytoremediation of heavy metal-contaminated soil.

Impacts of grazing exclusion on productivity partitioning along regional plant diversity and climatic gradients in Tibetan alpine grasslands

The biodiversity-productivity relationship is critical for better predicting ecosystem responses to climate change and human disturbance. However, it remains unclear about the effects of climate change, land use shifts, plant diversity, and their interactions on productivity partitioning above- and below-ground components in alpine grasslands on the Tibetan Plateau. To answer this question, we conducted field surveys at 33 grazed vs. fenced paired sites that are distributed across the alpine meadow, steppe, and desert-steppe zones on the northern Tibetan Plateau in early August of 2010-2013. Generalized additive models (GAMs) showed that aboveground net primary productivity (ANPP) linearly increased with growing season precipitation (GSP) while belowground net primary productivity (BNPP) decreased with growing season temperature (GST). Compared to grazed sites, short-term fencing did not alter the patterns of ANPP along climatic gradients but tended to decrease BNPP at moderate precipitation levels of 200 mm < GSP <450 mm. We also found that ANPP and BNPP linearly increased with species richness, ANPP decreased with Shannon diversity index, and BNPP did not correlate with the Shannon diversity index. Fencing did not alter the relationships between productivity components and plant diversity indices. Generalized additive mixed models furtherly confirmed that the interaction of localized plant diversity and climatic condition nonlinearly regulated productivity partitioning of alpine grasslands in this area. Finally, structural equation models (SEMs) revealed the direction and strength of causal links between biotic and abiotic variables within alpine grassland ecosystems. ANPP was controlled directly by GSP (0.53) and indirectly via species richness (0.41) and Shannon index (-0.12). In contrast, BNPP was influenced directly by GST (-0.43) and indirectly by GSP via species richness (0.05) and Shannon index (-0.02). Therefore, we recommend using a joint approach of GAMs and SEMs for better understanding mechanisms behind the relationship between biodiversity and ecosystem function under climate change and human disturbance.

Active and total microbial community dynamics and the role of functional genes bamA and mcrA during anaerobic digestion of phenol and p-cresol

The aim of the present work was to investigate the dynamics of microbial community at DNA and RNA level and the role of bamA and mcrA gene during anaerobic digestion of phenol and p-cresol. Anaerobic digestion was conducted in batch reactors and microbial community dynamics was analysed. Results showed that active microbial community was quite dissimilar in comparison to the total microbial community. Syntrophorhabdus and Bacillus were the dominant active bacterial genera whereas Methanosaeta together with Methanobacterium showed the highest potential activity in the Archaea domain indicating a relevant role of these microorganisms in the anaerobic process. Ecological Networks revealed dissimilar interactions at DNA and RNA level, being the latter a better descriptor of the known roles of dominant OTUs. QRT-PCR results showed that expression of bamA gene correlated positively with instantaneous degradation rate proving for first time its functionality and its relationship with the kinetics of the process.

Highly modular pattern in ant-plant interactions involving specialized and non-specialized myrmecophytes

Because Tachia guianensis (Gentianaceae) is a "non-specialized myrmecophyte" associated with 37 ant species, we aimed to determine if its presence alters the ant guild associated with sympatric "specialized myrmecophytes" (i.e., plants sheltering a few ant species in hollow structures). The study was conducted in a hilly zone of a neotropical rainforest where two specialized myrmecophytes grow at the bottom of the slopes, another at mid-slope, and a fourth on the hilltops. Tachia guianensis, which occurred everywhere, had its own guild of associated ant species. A network analysis showed that its connections with the four other myrmecophytes were rare and weak, the whole resulting in a highly modular pattern of interactions with one module (i.e., subnetwork) per myrmecophyte. Three ant species parasitized three out of the four specialized myrmecophytes (low nestedness noted), but were not or barely associated with T. guianensis that therefore did not influence the parasitism of specialized myrmecophytes.

Deciphering the core fouling-causing microbiota in a membrane bioreactor: Low abundance but important roles

Currently, membrane biofouling in membrane bioreactors (MBRs) is normally attributed to the occurrence of abundant bacterial species on membranes, whereas the roles of low-abundance bacteria have not been paid sufficient attention. In this study, the linear discriminant analysis (LDA) effect size (LEfSe) algorithm was used to identify active biomarkers, determining 67 different phylotypes among Bulk sludge, low-fouling Bio-cake (10 kPa), high-fouling Bio-cake (25 kPa) and Membrane pore in a membrane bioreactor with NaOCl backwash. Interestingly, a large proportion of the active biomarkers in bio-cake samples, such as Methylophilaceae, Burkholderiaceae, Paucibacter and Pseudoxanthomonas, did not fall within the abundant taxa (i.e., <0.05% relative abundance), indicating the preferential growth of these low-abundance bacteria on the membrane surface. Furthermore, the characterization of microbial interactions using a random matrix theory (RMT)-based network approach obtained a network consisting of 120 nodes and 228 edges. Specifically, network analysis showed the presence of an intense competition among bacterial species in the fouling-related communities, suggesting that negative interactions have an important effect on determining the microbial community structure. More importantly, the LEfSe algorithm and network analysis showed that most of the core species of the bio-cake, such as Burkholderiaceae, Bacillus and Rhodothermaceae, merely amounted to a very low relative abundance (<1%), suggesting their unrecognized and over-proportional ecological role in triggering the initial biofilm formation and subsequent biofilm maturation during MBR operation. Overall, this work should improve our understanding of the bacterial community structure on the fouled membranes in MBRs.

Health risk assessment of heavy metals in fish and accumulation patterns in food web in the upper Yangtze River, China

This study aims to concern the distribution of As, Cr, Cd, Hg, Cu, Zn, Pb and Fe in surface sediment, zoobenthos and fishes, and quantify the accumulative ecological risk and human health risk of metals in river ecological system based on the field investigation in the upper Yangtze River. The results revealed high ecological risk of As, Cd, Cu, Hg, Zn and Pb in sediment. As and Cd in fish presented potential human health risk of metals by assessing integrated target hazard quotient results based on average and maximum concentrations, respectively. No detrimental health effects of heavy metals on humans were found by daily fish consumption. While, the total target hazard quotient (1.659) exceeding 1, it meant that the exposed population might experience noncarcinogenic health risks from the accumulative effect of metals. Ecological network analysis model was established to identify the transfer routes and quantify accumulative effects of metals on river ecosystem. Control analysis between compartments showed large predator fish firstly depended on the omnivorous fish. Accumulative ecological risk of metals indicated that zoobenthos had the largest metal propagation risk and compartments located at higher trophic levels were not easier affected by the external environment pollution.

CAPSULE

A potential accumulative ecological risk of heavy metal in the food web was quantified, and the noncarcinogenic health risk of fish consumption was revealed for the upper reach of the Yangtze River.

Food Web Designer: a flexible tool to visualize interaction networks

Species are embedded in complex networks of ecological interactions and assessing these networks provides a powerful approach to understand what the consequences of these interactions are for ecosystem functioning and services. This is mandatory to develop and evaluate strategies for the management and control of pests. Graphical representations of networks can help recognize patterns that might be overlooked otherwise. However, there is a lack of software which allows visualizing these complex interaction networks. Food Web Designer is a stand-alone, highly flexible and user friendly software tool to quantitatively visualize trophic and other types of bipartite and tripartite interaction networks. It is offered free of charge for use on Microsoft Windows platforms. Food Web Designer is easy to use without the need to learn a specific syntax due to its graphical user interface. Up to three (trophic) levels can be connected using links cascading from or pointing towards the taxa within each level to illustrate top-down and bottom-up connections. Link width/strength and abundance of taxa can be quantified, allowing generating fully quantitative networks. Network datasets can be imported, saved for later adjustment and the interaction webs can be exported as pictures for graphical display in different file formats. We show how Food Web Designer can be used to draw predator-prey and host-parasitoid food webs, demonstrating that this software is a simple and straightforward tool to graphically display interaction networks for assessing pest control or any other type of interaction in both managed and natural ecosystems from an ecological network perspective.

Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation

β-glucan is a prebiotic well known for its beneficial outcomes on sea cucumber health through modifying the host intestinal microbiota. High-throughput sequencing techniques provide an opportunity for the identification and characterization of microbes. In this study, we investigated the intestinal microbial community composition, interaction among species, and intestinal immune genes in sea cucumber fed with diet supplemented with or without β-glucan supplementation. The results show that the intestinal dominant classes in the control group are Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, whereas Alphaproteobacteria, Flavobacteriia, and Verrucomicrobiae are enriched in the β-glucan group. Dietary β-glucan supplementation promoted the proliferation of the family Rhodobacteraceae of the Alphaproteobacteria class and the family Verrucomicrobiaceae of the Verrucomicrobiae class and reduced the relative abundance of the family Flavobacteriaceae of Flavobacteria class. The ecological network analysis suggests that dietary β-glucan supplementation can alter the network interactions among different microbial functional groups by changing the microbial community composition and topological roles of the OTUs in the ecological network. Dietary β-glucan supplementation has a positive impact on immune responses of the intestine of sea cucumber by activating NF-κB signaling pathway, probably through modulating the balance of intestinal microbiota.

Ecological network analysis of an urban metabolic system based on input-output tables: model development and case study for Beijing

If cities are considered as "superorganisms", then disorders of their metabolic processes cause something analogous to an "urban disease". It is therefore helpful to identify the causes of such disorders by analyzing the inner mechanisms that control urban metabolic processes. Combining input-output analysis with ecological network analysis lets researchers study the functional relationships and hierarchy of the urban metabolic processes, thereby providing direct support for the analysis of urban disease. In this paper, using Beijing as an example, we develop a model of an urban metabolic system that accounts for the intensity of the embodied ecological elements using monetary input-output tables from 1997, 2000, 2002, 2005, and 2007, and use this data to compile the corresponding physical input-output tables. This approach described the various flows of ecological elements through urban metabolic processes and let us build an ecological network model with 32 components. Then, using two methods from ecological network analysis (flow analysis and utility analysis), we quantitatively analyzed the physical input-output relationships among urban components, determined the ecological hierarchy of the components of the metabolic system, and determined the distribution of advantage-dominated and disadvantage-dominated relationships, thereby providing scientific support to guide restructuring of the urban metabolic system in an effort to prevent or cure urban "diseases".

Theory of interface: category theory, directed networks and evolution of biological networks

Biological networks have two modes. The first mode is static: a network is a passage on which something flows. The second mode is dynamic: a network is a pattern constructed by gluing functions of entities constituting the network. In this paper, first we discuss that these two modes can be associated with the category theoretic duality (adjunction) and derive a natural network structure (a path notion) for each mode by appealing to the category theoretic universality. The path notion corresponding to the static mode is just the usual directed path. The path notion for the dynamic mode is called lateral path which is the alternating path considered on the set of arcs. Their general functionalities in a network are transport and coherence, respectively. Second, we introduce a betweenness centrality of arcs for each mode and see how the two modes are embedded in various real biological network data. We find that there is a trade-off relationship between the two centralities: if the value of one is large then the value of the other is small. This can be seen as a kind of division of labor in a network into transport on the network and coherence of the network. Finally, we propose an optimization model of networks based on a quality function involving intensities of the two modes in order to see how networks with the above trade-off relationship can emerge through evolution. We show that the trade-off relationship can be observed in the evolved networks only when the dynamic mode is dominant in the quality function by numerical simulations. We also show that the evolved networks have features qualitatively similar to real biological networks by standard complex network analysis.

Qualitative community stability determines parasite establishment and richness in estuarine marshes

The establishment of parasites with complex life cycles is generally thought to be regulated by free-living species richness and the stability of local ecological interactions. In this study, we test the prediction that stable host communities are prerequisite for the establishment of complex multi-host parasite life cycles. The colonization of naïve killifish, Fundulus heteroclitus, by parasites was investigated in 4 salt marsh sites that differed in time since major ecological restoration, and which provided a gradient in free-living species richness. The richness of the parasite community, and the rate at which parasite species accumulated in the killifish, were similar between the low diversity unrestored site and the two high diversity (10- and 20-year) restored marsh sites. The parasite community in the newly restored marsh (0 year) included only directly-transmitted parasite species. To explain the paradox of a low diversity, highly invaded salt marsh (unrestored) having the same parasite community as highly diverse restored marsh sites (10 and 20 yrs) we assessed qualitative community stability. We find a significant correlation between system stability and parasite species richness. These data suggest a role for local stability in parasite community assembly, and support the idea that stable trophic relationships are required for the persistence of complex parasite life cycles.

More than a meal… integrating non-feeding interactions into food webs

Organisms eating each other are only one of many types of well documented and important interactions among species. Other such types include habitat modification, predator interference and facilitation. However, ecological network research has been typically limited to either pure food webs or to networks of only a few (<3) interaction types. The great diversity of non-trophic interactions observed in nature has been poorly addressed by ecologists and largely excluded from network theory. Herein, we propose a conceptual framework that organises this diversity into three main functional classes defined by how they modify specific parameters in a dynamic food web model. This approach provides a path forward for incorporating non-trophic interactions in traditional food web models and offers a new perspective on tackling ecological complexity that should stimulate both theoretical and empirical approaches to understanding the patterns and dynamics of diverse species interactions in nature.