Vertical variations and environmental heterogeneity drove the symphony of periphytic protozoan fauna in marine ecosystems

Periphytic protozoa are esteemed icons of microbial fauna, renowned for their sensitivity and role as robust bioindicators, pivotal for assessing ecosystem stress and anthropogenic impacts on water quality. Despite their significance, research exploring the community dynamics of protozoan fauna across diverse water columns and depths in shallow waters has been notably lacking. This is the first study that examines the symphony of protozoan fauna in different water columns at varying depths (1, 2, 3.5 and 5 m), in South China Sea. Our findings reveal that vertical changes and environmental heterogeneity plays pivotal role in shaping the protozoan community structure, with distinct preferences observed in spirotrichea and phyllopharyngea classes at specific depths. Briefly, diversity metrics (i.e., both alpha and beta) showed significantly steady patterns at 2 m and 3.5 m depths as well as high homogeneity in most of the indices was observed. Co-associations between environmental parameters and protozoan communities demonstrated temperature, dissolved oxygen, salinity, and pH, are significant drivers discriminating species richness and evenness across all water columns. Noteworthy variations of the other environmental parameters such as SiO3-Si, PO4--P, and NO2--N at 1 m and NO3--N, and NH4+-N, at greater depths, signal the crucial role of nutrient dynamics in shaping the protozoan communities. Moreover, highly sensitive species like Anteholosticha pulchara, Apokeronopsis crassa, and Aspidisca steini in varying environmental conditions among vertical columns may serve as eco- indicators of water quality. Collectively, this study contributes a thorough comprehension of the fine-scale structure and dynamics of protozoan fauna within marine ecosystems, providing insightful perspectives for ecological and water quality assessment in ever-changing marine environments.

Geographic distribution of bacterial communities of inland waters in China

Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.

The large-scale expansion of rubber plantations in southern India: major impacts and the changing nature of drivers

This study investigates the major environmental and socio-economic impacts of an increase in the area of rubber plantations and the changing patterns of drivers of land use changes. Using a combination of geospatial techniques and socio-economic methods, we mainly analyzed the rate of increase in area under rubber plantations, the major impacts of land use changes, and the changing drivers of land use changes. Our results show that the area under rubber plantations has increased significantly within the study area, with the area under rubber plantations increasing from 30 to 74% of the total area within five decades. Impact assessment of land use changes based on household surveys showed significant improvement in the socio-economic conditions of the farmers, however, at the expense of severe environmental degradation. Our results also indicate that while areas under rubber plantations continue to increase, the drivers of land use changes have changed over time. Furthermore, it has been observed that in the past, many interventions prioritized social and economic development and placed less emphasis on the ecological stability of the region. Perceptions of farmers revealed that the effects of ecological fragility already affected the economic robustness of the whole area. Therefore, we conclude that government interventions to support additional rubber cultivation should also focus on ecosystem stabilization in order to minimize the risk of an ecological catastrophe that would significantly affect the economic prosperity of the region.

Environmental drivers of biogeography and community structure in a Mid-Atlantic estuary

Estuaries include some of the most productive yet anthropogenically impacted marine ecosystems on the planet, and provide critical habitat to many ecologically and economically important marine species. In order to elucidate ecological function in estuaries, we must understand what factors drive community dynamics. Delaware Bay is the third largest estuary in the United States and hosts over 200 species of migrant and resident fishes and invertebrates. The Delaware Division of Fish and Wildlife has conducted two long-term trawl surveys at monthly intervals in Delaware Bay since 1966. The two surveys collect data on environmental conditions, species composition, and number of fishes and macroinvertebrates across different size classes and life histories. Using a suite of multivariate approaches including hierarchical cluster analysis, canonical correlation analysis, and permutational multivariate analysis of variance, we characterized the fish and macroinvertebrate community in Delaware Bay and found that community composition and environmental conditions varied across spatial and seasonal scales. We identified four distinct biogeographic regions, based on environmental conditions and community composition, which were consistent across surveys. We found that the community was driven primarily by gradients in temperature and salinity and that abundant, frequently occurring species in the Bay have well-defined environmental associations. Our work represents the first attempt to use an existing historical survey to better understand how environmental parameters influence diversity and distribution of macrofauna within Delaware Bay, providing insight into how abiotic variables, influenced by climate, may impact the Delaware Bay ecosystem and similar estuarine ecosystems worldwide.

Per- and polyfluoroalkyl substances in a subtropical river-mangrove estuary-bay system

Mangrove estuaries are one of the most economically valuable and biologically diverse coastal ecosystems. However, knowledge of emerging pollutants in mangrove estuaries is limited. This study provided insight into the PFAS in a river (Zhangjiang River, ZR)-mangrove estuary (Zhangjiang River Estuary, ZRE)-bay (Dongshan Bay, DSB) continuous system in Fujian Province, China. The Σ25PFAS (sum of 25 PFAS) concentrations (0.94 ∼ 62.44 ng/L) showed a declining trend from the river to bay. The Zhe-Min Coastal Current (ZMCC) can transport an abundance of PFAS, especially PFOA, from the northern sea to southern bays, which can affect the seasonal distribution of PFAS concentrations in the DSB and result in PFOA/Σ25PFAS with a decreasing trend in the DSB (28.08%), ZRE (21.15%), and ZR (14.13%), respectively. The primary PFAS sources in this area determined by the positive matrix factor model mainly contained the effluent of the wastewater treatment plant neighboring the R2 site, discharge of domestic and production wastewater, irregular emissions of aqueous film-forming foams, and fluorochemistry industry wastewater transmitted from the ZMCC. The PFAS pollution in the mangrove creek was mainly affected by the discharge of domestic and production wastewater and presented a significant point source pollution, especially during the rainy season.

Outdoor climate drives diversity patterns of dominant microbial taxa in caves worldwide

The cave microbiota is assumed to be shaped by indoor microclimate, biotic and abiotic factors, which are largely dependent from outside environmental conditions; however, this knowledge is available at local or regional scales only. To address this knowledge gap, we reanalyzed over 1050 bacterial and fungal communities of caves worldwide, and found that outdoor temperature and rainfall play a critical role in explaining differences in microbial diversity patterns of global caves, selecting specific dominant taxa across gradients of growing aridity conditions with arid climate leading to a reduction in total cave microbial diversity. Moreover, we found that fungal (from 186 to 1908 taxa) and bacterial (from 467 to 1619 taxa) diversity increased under temperate-tropical and temperate-continental climatic regions, respectively, highlighting an opposite preference for the two microbial compartments. We hypothesized that outdoor geographical, climatic variables and lithology are critical epistatic drivers in assembling microbial communities and their dominant taxa, whose ecological responses could be useful to predict the fate of these subterranean environments in the context of climate change. Our work elucidates the intimate connection between caves microbiota and surface ecosystems highlighting the sensitivity of cave microbial communities to climatic changes and environmental degradation. This work also provides a natural benchmark for the biogeographic information for caves globally and for protection strategies aiming at conservation of underground environments.

Camera traps reveal a high prevalence of sarcoptic mange in red foxes from northern Spain

The mite Sarcoptes scabiei affects numerous mammal species causing the sarcoptic mange, a widespread disease with relevance for wildlife conservation, welfare, and management. The red fox (Vulpes vulpes) could become infested by direct and indirect routes leading to external skin lesions potentially recognizable by devices such as camera traps (CTs). In the present study, 86 randomly placed CTs were used to investigate the apparent prevalence and severity of S. scabiei in a red fox population from northern Spain. Their potential environmental and population-related drivers were also assessed. A total of 341 independent encounters were examined to visually identify mange-compatible lesions. The apparent prevalence was 19.16% (confidence interval (CI) 95%: 15.08-23.80) of which 82.81% (CI95%: 71.33-91.10) were severe. Our results revealed that habitat attributes such as lower altitudes, higher coverage of water-linked habitats and woodland predominance, were significant predictors of the apparent risk of mange. The models also suggested that the apparent prevalence of mange was associated with poor body condition and elevated frequencies of spatial coincidence among fox encounters, which facilitates indirect transmission. Interestingly, we did not observe mange-compatible lesions in other sympatric wild species (>15,000 encounters examined). This could be explained by the mite's host specificity and the low probability that these other potential hosts use sites where transmission among foxes usually occurs, such as dens. This study illustrates how camera trapping can be used as an interesting tool for the surveillance of wildlife diseases, thus overcoming the logistic constraints derived from direct sampling and allowing the early detection and better management of pathogens in the riskiest areas.

Physical, biological and anthropogenic drivers of spatial patterns of coral reef fish assemblages at regional and local scales

Species abundance, diversity and community assemblage structure are determined by multiple physical, habitat and management drivers that operate across multiple spatial scales. Here we used a multi-scale coral reef monitoring dataset to examine regional and local differences in the abundance, species richness and composition of fish assemblages in no-take marine reserve (NTMR) and fished zones at four island groups in the Great Barrier Reef Marine Park, Australia. We applied boosted regression trees to quantify the influence of 20 potential drivers on the coral reef fish assemblages. Reefs in two locations, Magnetic Island and the Keppel Islands, had distinctive fish assemblages and low species richness, while the Palm and Whitsunday Islands had similar species composition and higher species richness. Overall, our analyses identified several important physical (temperature, wave exposure) and biological (coral, turf, macroalgal and unconsolidated substratum cover) drivers of inshore reef fish communities, some of which are being altered by human activities. Of these, sea surface temperature (SST) was more influential at large scales, while wave exposure was important both within and between island groups. Species richness declined with increasing macroalgal cover and exposure to cyclones, and increased with SST. Species composition was most strongly influenced by mean SST and percent cover of macroalgae. There was substantial regional variation in the local drivers of spatial patterns. Although NTMR zoning influenced total fish density in some regions, it had negligible effects on fish species richness, composition and trophic structure because of the relatively small number of species targeted by the fishery. These findings show that inshore reef fishes are directly influenced by disturbances typical of the nearshore Great Barrier Reef, highlighting the need to complement global action on climate change with more targeted localised efforts to maintain or improve the condition of coral reef habitats.

management

Agriculture is the main contributor to anthropogenic nitrous oxide (N2O) and methane (CH4) emissions. Therefore, mitigation options are urgently needed. In contrast to carbon dioxide, eddy covariance measurements of N2O and CH4 fluxes are still scarce, and thus little is known how environmental and biotic drivers as well as management affect the net N2O and CH4 exchange in grasslands. Thus, we investigated the most important drivers of net ecosystem N2O and CH4 fluxes in a temperate grassland, and continued a N2O mitigation experiment (increased clover proportion vs. fertilization with slurry). Random forest gap-filling models were able to capture intermittent emission peaks, performing better for half-hourly N2O than for CH4 fluxes. The unfertilized clover parcel (parcel B) continued to show lower N2O emissions (4.4 and 2.7 kg N2O-N ha-1 yr-1) compared to the fertilized parcel (parcel A; 6.9 and 5.9 kg N2O-N ha-1 yr-1) for 2019 and 2020, respectively. Tier 1 nitrogen (N) emission factors of 2.6 % and 1.9 % were observed at the fertilized parcel during the study period. Lower soil N concentrations indicated a lower N leaching risk at the clover than at the fertilized parcel. Annual CH4 emissions (including periods with sheep grazing) were similar from both parcels, and ranged from 25 to 38.5 kg CH4-C ha-1. The most important drivers of both N2O and CH4 fluxes were lagged precipitation and water filled pore space, but also management (for N2O from parcel B; CH4 from parcel A). Biotic variables such as vegetation height and leaf area index were important predictors for the N2O exchange, while grazing temporarily increased CH4 emissions. Overall, reducing N fertilization and increasing the legume proportion were effective N2O reduction measures. In particular, adjusting N fertilization to plant N demands can help to avoid high N2O emissions from grasslands.

Seasonal changes characterise the shark and ray assemblages in a subtropical shallow sandy habitat in the iSimangaliso Wetland Park, South Africa

Understanding how environmental drivers influence shark and ray spatial and temporal patterns can provide crucial knowledge for their evidence-based protection and long-term monitoring. However, information on which drivers of variation are most important for elasmobranch communities on soft sediments is limited. Using baited remote underwater stereo-video systems (stereo-BRUVs), we investigated how seasonal and environmental variables affected the elasmobranchs of the iSimangaliso Wetland Park marine protected area (MPA) in South Africa (SA). In total, 11 species were identified from 48 sites between 12 m and 33 m water depth in a sandy habitat. While species richness was similar across seasons, the total abundance of elasmobranchs recorded was higher in winter than summer. The species assemblage composition varied significantly between seasons, with the Human's whaler shark Carcharhinus humani prevalent in summer and the Critically Endangered whitespotted wedgefish Rhynchobatus djiddensis more abundant during winter. Most species were sighted throughout the entire depth range, but rays were more common in shallower waters (< 25 m depth), while C. humani and R. djiddensis were more common in the deeper depth zone of this study. This research provides baseline information about this previously unexplored sandy habitat for elasmobranchs in a site of regional and global significance. Records of species of conservation concern in the sampling area highlight the importance of protecting sand environments within an MPA.

What drives the recruitment of European sardine in Atlanto-Iberian waters (SW Europe)? Insights from a 22-year analysis

The European sardine (Sardina pilchardus) is the most abundant and socio-economically important small pelagic fish species in Western Iberia Upwelling Ecosystem. As a result of a long series of low recruitments, sardine biomass off Western Iberia has greatly reduced since the 2000s. Recruitment of small pelagic fish is mainly dependent on environmental factors. In order to identify the key drivers of sardine recruitment, it is essential to understand its temporal and spatial variability. To achieve this goal, a comprehensive suite of atmospheric, oceanographic, and biological variables spanning 1998-2020 (22 years) were extracted from satellite datasets. These were then related to in situ recruitment estimates obtained from yearly spring acoustic surveys carried out along two different hotspots of sardine recruitment of the southern Iberian sardine stock (NW Portugal and Gulf of Cadiz). Sardine recruitment in Atlanto-Iberian waters appears to be driven by distinct combinations of environmental factors, although sea surface temperature was identified as the main driver in both regions. Physical conditions that favour larval feeding and retention, such as shallower mixed layers and onshore transport, were also seen to play a vital role in modulating sardine recruitment. Furthermore, high sardine recruitment in NW Iberia was associated with optimal conditions in the winter (January-February). In contrast, recruitment strength of sardine off the Gulf of Cadiz were associated with the optimal conditions during late autumn and spring. The results from this work provide valuable insights to further understand the dynamics of sardine off Iberia, with potential to contribute to the sustainable management of sardine stocks in Atlanto-Iberian waters, particularly under climate change.

Biogeographic distribution, ecotype partitioning and controlling factors of Chloroflexi in the sediments of six hadal trenches of the Pacific Ocean

The hadal trenches are "hot spots" for mineralization of organic matter in the deep ocean. Chloroflexi are one of the most dominant and active taxa in trench sediments, serving as important drivers of carbon cycles in hadal trenches. However, current understanding on hadal Chloroflexi is largely restricted to individual trench. This study systematically analyzed the diversity, biogeographic distribution, ecotype partitioning as well as environmental drivers of Chloroflexi in the sediments of hadal trenches, by reanalyzing 16S rRNA gene libraries of 372 samples from 6 trenches around the Pacific Ocean. The results showed that Chloroflexi averagely account for 10.10 % and up to 59.95 % of total microbial communities in the trench sediments. Positive correlations between relative abundance of Chloroflexi and depths down the vertical sediment profiles were observed in all of the sediment cores analyzed, suggesting the increasing significance of Chloroflexi in deeper sediment layers. Overall, trench sediment Chloroflexi were mainly composed of the classes Dehalococcidia, Anaerolineae and JG30-KF-CM66, and four orders i.e. SAR202, Anaerolineales, norank JG30-KF-CM66 and S085, were identified as core taxa that were dominant and prevalent in the hadal trench sediments. A total of 22 subclusters were identified within these core orders, and distinct patterns of ecotype partitioning related with depths down the vertical sediment profiles were observed, suggesting the great diversification of metabolic potentials and environment preference of different Chloroflexi lineages. The spatial distribution of hadal Chloroflexi were found to be significantly related with multiple environmental factors, while depths down the vertical sediment profiles explained the highest proportion of variations. These results provide valuable information for further exploring the roles of Chloroflexi in biogeochemical cycle of the hadal zone, and lay the foundation for understanding the adaptive mechanisms and evolutionary characteristics of microorganisms in hadal trenches.

Metagenomic analysis to determine the characteristics of antibiotic resistance genes in typical antibiotic-contaminated sediments

Comprehensive studies of the effects of various physical and chemical variables (including heavy metals), antibiotics, and microorganisms in the environment on antibiotic resistance genes are rare. We collected sediment samples from the Shatian Lake aquaculture area and surrounding lakes and rivers located in Shanghai, China. The spatial distribution of sediment ARGs was assessed by metagenomic analysis that revealed 26 ARG types (510 subtypes), dominated by Multidrug, β-lactam, Aminoglycoside, Glycopeptides, Fluoroquinolone, and Tetracyline. Redundancy discriminant analysis indicated that antibiotics (SAs and MLs) in the aqueous environment and sediment along with water TN and TP were the key variables affecting the abundance distribution of total ARGs. However, the main environmental drivers and key influences differed among the different ARGs. For total ARGs, the environmental subtypes affecting their structural composition and distribution characteristics were mainly antibiotic residues. Procrustes analysis showed a significant correlation between ARGs and microbial communities in the sediment in the survey area. Network analysis revealed that most of the target ARGs were significantly and positively correlated with microorganisms, and a small number of ARGs (e.g., rpoB, mdtC, and efpA) were highly significantly and positively correlated with microorganisms (e.g., Knoellia, Tetrasphaera, and Gemmatirosa). Potential hosts for the major ARGs included Actinobacteria, Proteobacteria, and Gemmatimonadetes. Our study provides new insight and a comprehensive assessment of the distribution and abundance of ARGs and the drivers of ARG occurrence and transmission.

Twenty-year record of white pox disease in the Florida Keys: importance of environmental risk factors as drivers of coral health

Declining coral populations worldwide place a special premium on identifying risks and drivers that precipitate these declines. Understanding the relationship between disease outbreaks and their drivers can help to anticipate when the risk of a disease pandemic is high. Populations of the iconic branching Caribbean elkhorn coral Acropora palmata have collapsed in recent decades, in part due to white pox disease (WPX). To assess the role that biotic and abiotic factors play in modulating coral disease, we present a predictive model for WPX in A. palmata using 20 yr of disease surveys from the Florida Keys plus environmental information collected simultaneously in situ and via satellite. We found that colony size was the most influential predictor for WPX occurrence, with larger colonies being at higher risk. Water quality parameters of dissolved oxygen saturation, total organic carbon, dissolved inorganic nitrogen, and salinity were implicated in WPX likelihood. Both low and high wind speeds were identified as important environmental drivers of WPX. While high temperature has been identified as an important cause of coral mortality in both bleaching and disease scenarios, our model indicates that the relative influence of HotSpot (positive summertime temperature anomaly) was low and actually inversely related to WPX risk. The predictive model developed here can contribute to enabling targeted strategic management actions and disease surveillance, enabling managers to treat the disease or mitigate disease drivers, thereby suppressing the disease and supporting the persistence of corals in an era of myriad threats.

Copper and temperature shaped abundant and rare community assembly respectively in the Yellow River

Untangling assembly and microbial interaction of abundant and rare microbiota in aquatic ecosystem is pivotal for understanding how community assembly respond to environmental variables and co-occurrence patterns. Here, we explored the assembly mechanisms, their drivers, and species co-occurrence of abundant and rare microbiomes in the Yellow River using 16S rRNA gene sequencing in Lanzhou, China. Here, abundant community was ubiquitous across all sites, whereas rare community was uneven distributed. The richness and community dissimilarity of rare taxa were significantly greater than those of abundant ones. Stochastic processes structured the rare community assembly in spring and winter, while deterministic processes shaped the abundant and rare community assembly in other seasons and all sites. Copper and water temperature mediated the balance between deterministic and stochastic processes of abundant and rare community, respectively. A few abundant taxa with closer relationships frequently occupied central positions and had a great effect on other co-occurrences in the network, while the majority of keystone microbiota were rare microbiome and played a considerable part in maintaining the network structure. Our study provides some ecological proposals for water quality management and ecological stability of the Yellow River. KEY POINTS: • Deterministic process dominated abundant and rare community assembly. • Cu and TW mediated the balance of abundant and rare community assembly respectively. • Abundant taxa had a greater effect on other co-occurrences in the network.

Greenhouse gas emissions and environmental drivers in different natural wetland regions of China

Wetlands sequestrate carbon at the highest rate than any other ecosystems on Earth. However, the spatial and temporal dynamics of GHGs emissions from the wetland ecosystems in China are still elusive. We synthesized 166 publications that contain 462 in situ measurements of GHGs emissions from the natural wetlands in China, and further analyzed the variability and the drivers of GHGs emissions in eight subdivisions of China's wetlands. The results show that the current studies are mainly concentrated in the estuaries, Sanjiang Plain, and Zoige wetlands. The average CO₂ emissions, CH₄ fluxes and N₂O fluxes from Chinese wetlands were 218.84 mg·m^-2·h^-1, 1.95 mg·m^-2·h^-1 and 5.8 × 10^-2 mg·m^-2·h^-1, respectively. The global warming potential (GWP) of China's wetlands was estimated to be 1881.36 TgCO₂-eq·yr^-1, with CO₂ emissions contributing more than 65% to the GWP value. The combined GWP values of Qinghai-Tibet Plateau wetlands, coastal wetlands and northeastern wetlands account for 84.8% of GWP of China's wetlands. Correlation analysis showed that CO₂ emissions increased with the increasing mean annual temperature, elevation, annual rainfall, and wetland water level, but decreased with soil pH. CH₄ fluxes increased with the mean annual temperature and soil water content but decreased with the redox potential. This study analyzed the drivers of GHGs emissions from wetland ecosystems at the national scale, and GWP values of eight wetland subregions of China were comprehensively assessed. Our results are potentially useful for the global GHGs inventory, and can help assess the response of GHGs emissions of wetland ecosystem to environmental and climate change.

Vector communities under global change may exacerbate and redistribute infectious disease risk

Vector-borne parasites may be transmitted by multiple vector species, resulting in an increased risk of transmission, potentially at larger spatial scales compared to any single vector species. Additionally, the different abilities of patchily distributed vector species to acquire and transmit parasites will lead to varying degrees of transmission risk. Investigation of how vector community composition and parasite transmission change over space due to variation in environmental conditions may help to explain current patterns in diseases but also informs our understanding of how patterns will change under climate and land-use change. We developed a novel statistical approach using a multi-year, spatially extensive case study involving a vector-borne virus affecting white-tailed deer transmitted by Culicoides midges. We characterized the structure of vector communities, established the ecological gradient controlling change in structure, and related the ecology and structure to the amount of disease reporting observed in host populations. We found that vector species largely occur and replace each other as groups, rather than individual species. Moreover, community structure is primarily controlled by temperature ranges, with certain communities being consistently associated with high levels of disease reporting. These communities are essentially composed of species previously undocumented as potential vectors, whereas communities containing putative vector species were largely associated with low levels, or even absence, of disease reporting. We contend that the application of metacommunity ecology to vector-borne infectious disease ecology can greatly aid the identification of transmission hotspots and an understanding of the ecological drivers of parasite transmission risk both now and in the future.

Modeling the enigma of complex disease etiology

BACKGROUND

Complex diseases often present as a diagnosis riddle, further complicated by the combination of multiple phenotypes and diseases as features of other diseases. With the aim of enhancing the determination of key etiological factors, we developed and tested a complex disease model that encompasses diverse factors that in combination result in complex diseases. This model was developed to address the challenges of classifying complex diseases given the evolving nature of understanding of disease and interaction and contributions of genetic, environmental, and social factors.

METHODS

Here we present a new approach for modeling complex diseases that integrates the multiple contributing genetic, epigenetic, environmental, host and social pathogenic effects causing disease. The model was developed to provide a guide for capturing diverse mechanisms of complex diseases. Assessment of disease drivers for asthma, diabetes and fetal alcohol syndrome tested the model.

RESULTS

We provide a detailed rationale for a model representing the classification of complex disease using three test conditions of asthma, diabetes and fetal alcohol syndrome. Model assessment resulted in the reassessment of the three complex disease classifications and identified driving factors, thus improving the model. The model is robust and flexible to capture new information as the understanding of complex disease improves.

CONCLUSIONS

The Human Disease Ontology's Complex Disease model offers a mechanism for defining more accurate disease classification as a tool for more precise clinical diagnosis. This broader representation of complex disease, therefore, has implications for clinicians and researchers who are tasked with creating evidence-based and consensus-based recommendations and for public health tracking of complex disease. The new model facilitates the comparison of etiological factors between complex, common and rare diseases and is available at the Human Disease Ontology website.

Microplastic pollution in small rivers along rural-urban gradients: Variations across catchments and between water column and sediments

The aquatic ecosystems of the world are highly burdened with microplastics (MPs; particles <5 mm). There is a great need for better understanding of patterns of MP pollution across catchments and rivers of different sizes, anthropogenic pressures and hydrogeomorphological features. In this study, we investigated the MP concentrations including their characteristics (polymer type, shape, size and colour), and MP distribution in water and sediments of two hydrogeomorphologically different small-scale catchments (< 800 km²), namely Kamniška Bistrica (KB) and Ljubljanica (LJ), Slovenia. The main objective of this study was to gain a better understanding of how WWTP effluents and catchment urbanisation together with the diversity of natural hydrogeomorphology, affect the quantity and quality of MP pollutants in the rivers with smaller catchments. Significantly different mean MP concentrations were found in the water columns (KB: 59 ± 16 items m^-3; LJ: 31 ± 14 items m^-3), but not in the sediments (KB: 22 ± 20 items kg^-1; LJ: 23 ± 25 items kg^-1). A longitudinal gradient with increasing particle concentration was observed in both water and sediment samples and in both catchments. Polyethylene (PE) and polypropylene (PP) particles dominated in all samples. Fibres were predominant in the water column samples, while fragments were more common in the sediment samples. MP particles were mostly coloured, and most of them were smaller than 2 mm in both water and sediment samples. The critical evaluation of the results and previous studies suggest that the characteristics of the catchment (anthropogenic pressures, size, climate, etc.), the hydrogeomorphology of the river (sediment type, discharge, flow velocity etc.), the sampling location along the river, the sampled compartment (water, sediment), the sampling method, and the hydrometeorological characteristics at the time of sampling, are important factors for observed MP concentrations and other characteristics.

Comprehensive assessment of dissolved organic matter processing in the Amazon River and its major tributaries revealed by positive and negative electrospray mass spectrometry and NMR spectroscopy

Rivers are natural biogeochemical systems shaping the fates of dissolved organic matter (DOM) from leaving soils to reaching the oceans. This study focuses on Amazon basin DOM processing employing negative and positive electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI[±] FT-ICR MS) and nuclear magnetic resonance spectroscopy (NMR) to reveal effects of major processes on the compositional space and structural characteristics of black, white and clear water systems. These include non-conservative mixing at the confluences of (1) Solimões and the Negro River, (2) the Amazon River and the Madeira River, and (3) in-stream processing of Amazon River DOM between the Madeira River and the Tapajós River. The Negro River (black water) supplies more highly oxygenated and high molecular weight compounds, whereas the Solimões and Madeira Rivers (white water) contribute more CHNO and CHOS molecules to the Amazon River main stem. Aliphatic CHO and abundant CHNO compounds prevail in Tapajos River DOM (clear water), likely originating from primary production. Sorption onto particles and heterotrophic microbial degradation are probably the principal mechanisms for the observed changes in DOM composition in the Amazon River and its tributaries.

Frequent observations of novel plastic forms in the Ariho River estuary, Honshu, Japan

Pyroplastic and plastiglomerate are novel plastic forms that are currently being reported from coastal beaches worldwide. Pyroplastic is burned plastic with a rock-like appearance. Plastiglomerate is a solid bond consisting of either melted plastic attached to rock (in-situ plastiglomerate) or a melted plastic matrix containing (in)organic material (clastic plastiglomerate). Both plastic forms have been related to the (un)intentional burning of plastic. Yet, information on pyroplastic and plastiglomerate from estuarine habitats is limited to a pilot study (for this study) and knowledge of pyroplastic and plastiglomerate dynamics as well as the underlying drivers is missing. To address these knowledge gaps, we frequently surveyed stranded pyroplastics and plastiglomerates in the Ariho River estuary (Honshu, Japan) over seven months and studied the collected samples at the lab. In total, 37 pyroplastics (consisting of polyethylene, polypropylene, polystyrene, alkyd resin, polyacrylate styrene and polyvinyl chloride) and seven plastiglomerates (consisting of polyethylene and polypropylene) occurred. While pyroplastics occurred frequently, plastiglomerates occurred occasionally which indicates that both forms are common. Pyroplastic (but not plastiglomerate) occurrence and density (items/m²) were related to intertidal elevation. Strandline pyroplastic density, that contributed heavily to the pyroplastic and plastiglomerate entirety, increased under prevailing onshore winds which shows that such winds are environmental drivers of pyroplastic density. Floating tests revealed that clastic plastiglomerate can float. Macro-, micro- and spectroscopic examinations indicated only slight pyroplastic and plastiglomerate weathering which suggests the regional and/or recent formation of both plastic forms. Additionally, we detected the first plastiglomerate with clastic and in-situ features (a plastic matrix containing (in)organic material firmly melted to a rock) which constituted a novel plastiglomerate subtype that we termed "clastic/in-situ plastiglomerate". Overall, our study initiates the development of the fundamental understandings of pyroplastic and plastiglomerate dynamics and the underlying drivers in estuaries.

Co-driving factors of tidal effect on the abundance and distribution of antibiotic resistance genes in the Yongjiang Estuary, China

The unreasonable use of antibiotics and the transmission of antibiotic resistance genes (ARGs) induced by antibiotics have led to a large number of ARGs entered the water environment, which seriously threatened human health and environmental safety. The estuarine aquatic environment connects with inland rivers and sea and is frequently influenced by human activities. This study aims to reveal the occurrences and abundances of ARGs and bacterial community composition by high-throughput quantitative PCR including 296 primers and high-throughput sequencing in the tide rising and ebbing of surface water in the Yongjiang Estuary, China. The results showed that there were a large number of ARGs and mobile genetic elements (MGEs) detected in the rising tide and ebb tide water bodies. The numbers of detected ARGs in each sample at rising and ebb tide ranged from 16 to 77 and 61 to 88, respectively, and the absolute abundance ranges were 1.69 × 10⁴-1.69 × 10⁹ copies/L and 3.18 × 10³-2.57 × 10⁹ copies/L, respectively. Obvious tidal distribution characteristics of ARGs were showed. Most of ARGs conferred resistance to multidrug, aminoglycosides and sulfanilamides. Proteobacteria, Actinobacteria and Bacteroidetes were the dominantly bacterial phylum in the Yongjiang Estuary. Network analysis results indicated that multi-genera were identified as possible ARGs hosts, and they carried more than two types of ARGs genes. Partial least squares path modeling further revealed that MGEs and bacterial community composition were the most important driving factors. The results of the study can provide the corresponding scientific basis for the diffusion and control of ARGs in estuaries.

Impact of dissolved organic matter and environmental factors on methylmercury concentrations across aquatic ecosystems inferred from a global dataset

Mercury (Hg) input into ecosystems is estimated to have increased by twofold to fivefold since the industrial revolution. In aquatic ecosystems, methylmercury (MeHg) receives the most attentions of all the Hg species due to its neurotoxicity and strong bioaccumulation capacity in food chain. Dissolved organic matter (DOM) is crucial in impacting aquatic Hg transformation. However, only few spatially constrained studies have attempted to quantify the relative importance of DOM and other factors (e.g., Hg availability, temperature, pH, and land-use type) on MeHg concentration. In this study, we collected data of 585 water samples at 373 sites globally, including lakes, rivers, estuaries, and wetlands, and characterized the global pattern of MeHg distribution and environmental drivers of aquatic MeHg concentration. Our results showed that MeHg concentrations ranged from detection limits to 11 (geometric mean 0.11 and average 0.29) ng/L, and the highest MeHg concentration and Hg methylation potential were observed in wetlands. A positive relationship was observed between MeHg fraction in the total mercury (THg) and DOM for all the aquatic ecosystems. Using the structural equation modeling, we found that Hg availability was a dominant factor in impacting water MeHg concentration followed by DOM. According to 129 samples of specific DOM source information, we found that the percentage of THg as MeHg (%MeHg) in water dominated by the autochthonous DOM was higher than that dominated by the allochthonous DOM. Our results could advance understanding of aquatic Hg cycling and their environmental drivers, which are fundamental for predicting and mitigating MeHg productions and its potential health risks for humans.

Multi-class secondary metabolites in cyanobacterial blooms from a tropical water body: Distribution patterns and real-time prediction

Cyanobacterial blooms that produce toxins occur in freshwaters worldwide and yet, the occurrence and distribution patterns of many cyanobacterial secondary metabolites particularly in tropical regions are still not fully understood. Moreover, predictive models for these metabolites by using easily accessible water quality indicators are rarely discussed. In this study, we investigated the co-occurrence and spatiotemporal trends of 18 well-known and less-studied cyanobacterial metabolites (including [D-Asp3] microcystin-LR (DM-LR), [D-Asp3] microcystin-RR (DM-RR), microcystin-HilR (MC-HilR), microcystin-HtyR (MC-HtyR), microcystin-LA (MC-LA), microcystin-LF (MC-LF), microcystin-LR (MC-LR), microcystin-LW (MC-LW), microcystin-LY (MC-LY), microcystin-RR (MC-RR) and microcystin-WR (MC-WR), Anatoxin-a (ATX-a), homoanatoxin-a (HATX-a), cylindrospermospin (CYN), nodularin (NOD), anabaenopeptin A (AptA) and anabaenopeptin B (AptB)) in a tropical freshwater lake often plagued with blooms. Random forest (RF) models were developed to predict MCs and CYN and assess the relative importance of 22 potential predictors that determined their concentrations. The results showed that 11 MCs, CYN, ATX-a, HATX-a, AptA and AptB were found at least once in the studied water body, with MC-RR and CYN being the most frequently occurring, intracellularly and extracellularly. AptA and AptB were detected for the first time in tropical freshwaters at low concentrations. The metabolite profiles were highly variable at both temporal and spatial scales, in line with spatially different phytoplankton assemblages. Notably, MCs decreased with the increase of CYN, possibly revealing interspecific competition of cyanobacteria. The rapid RF prediction models for MCs and CYN were successfully developed using 4 identified drivers (i.e., chlorophyll-a, total carbon, rainfall and ammonium for MCs prediction; and chloride, total carbon, rainfall and nitrate for CYN prediction). The established models can help to better understand the potential relationships between cyanotoxins and environmental variables as well as provide useful information for making policy decisions.

Phytoplankton dynamics in Louisiana estuaries: Building a baseline to understand current and future change

Louisiana estuaries are important habitats in the northern Gulf of Mexico, a region undergoing significant and sustained human- and climate-driven changes. This paper synthesizes data collected over multiple years from four Louisiana estuaries - Breton Sound, Terrebonne Bay, the Atchafalaya River Delta Estuary, and Vermilion Bay - to characterize trends in phytoplankton biomass, community composition, and the environmental factors influencing them. Results highlight similarities in timing and composition of maximum chlorophyll, with salinity variability often explaining biomass trends. Distinct drivers for biomass versus community structure were observed in all four estuarine systems. Systems shared a lack of significant correlation between river discharge and overall phytoplankton biomass, while discharge was important for understanding community composition. Temperature was a significant explanatory variable for both biomass and community composition in only one system. These results provide a regional view of phytoplankton dynamics in Louisiana estuaries critical to understanding and predicting the effects of ongoing change.

Temporal variations in fecal indicator bacteria in bathing water and sediment in a coastal ecosystem (Aytré Bay, Charente-Maritime, France)

This study presents the fecal contamination dynamic at the two bathing sites of Aytré Bay (Charente Maritime, France). We quantified fecal indicator bacteria (FIB) abundances (Escherichia coli and enterococci) from water and sediment samples over one-year survey. Then we measured biological (bacterial abundance, chlorophyll-a), physico-chemical (dissolved nutrients and oxygen, salinity, pH …) and climatic (temperatures, rainfall and tidal coefficient) parameters. Results showed that FIB abundances were occasionally higher than the European regulatory threshold during winter, summer and fall. The "poor quality" of the bathing water was due to high enterococci abundance. We found negative significant correlations between FIB and water temperature and salinity, and positive significant correlations between FIB and rainfall, PO₄, NO₃, NO₂, and SiO₂ mainly in water. Relationships between parameters showed that during summer and spring the main environmental drivers were temperature and salinity, while in fall and winter they were rainfall and dissolved nutrients.

Co-occurrence of multiple cyanotoxins and taste-and-odor compounds in the large eutrophic Lake Taihu, China: Dynamics, driving factors, and challenges for risk assessment

Cyanobacterial blooms producing toxic metabolites occur frequently in freshwater, yet the environmental behaviors of complex cyanobacterial metabolites remain largely unknown. In this study, the seasonal and spatial variations of several classes of cyanotoxins (microcystins, cylindrospermopsins, saxitoxins) and taste-and-odor (T&O) compounds (β-cyclocitral, β-ionone, geosmin, 2-methylisoborneol) in Lake Taihu were simultaneously investigated for the first time. The total cyanotoxins were dominated by microcystins with concentrations highest in November (mean 2209 ng/L) and lowest in February (mean 48.7 ng/L). Cylindrospermopsins were abundant in May with the highest content of 622.8 ng/L. Saxitoxins only occurred in May (mean 19.2 ng/L) and November (mean 198.5 ng/L). Extracellular T&O compounds were most concentrated in August, the highest being extracellular β-cyclocitral (mean 240.6 ng/L) followed by 2-methylisoborneol (mean 146.6 ng/L). Environment variables play conflicting roles in modulating the dynamics of different groups of cyanotoxins and T&O compounds. Total phosphorus (TP), total nitrogen (TN), chlorophyll-a and cyanobacteria density were important factors affecting the variation of total microcystins, β-cyclocitral and β-ionone concentrations. In contrast, total cylindrospermopsins, 2-methylisoborneol and geosmin concentrations were significantly influenced by water temperature and TP. There was a significant and linear relationship between microcystins and β-cyclocitral/β-ionone, while cylindrospermopsins were positively correlated with 2-methylisoborneol and geosmin. The perceptible odors may be good indicators for the existence of cyanotoxins. Hazard quotients revealed that potential human health risks from microcystins were high in August and November. Meanwhile, the risks from cylindrospermopsins were at moderate levels. Cylindrospermopsins and saxitoxins were first identified in this lake, suggesting that diverse cyanotoxins might co-occur more commonly than previously thought. Hence, the risks from other cyanotoxins beyond microcystins shouldn't be ignored. This study also highlights that the necessity for further assessing the combination effects of these complex metabolites.

The relative importance of environmental factors in predicting phytoplankton shifting and cyanobacteria abundance in regulated shallow lakes

The phytoplankton community can be affected by multiple environmental factors such as climate, meteorology, hydrology, nutrients, and grazing. The complex interactive effects of these environmental factors as well as the resilience of phytoplankton communities further make the prediction of phytoplankton communities' dynamics challenging. In this study, we analyzed multiple environmental factors and their relative importance in predicting both phytoplankton shifting and cyanobacteria abundance in two regulated shallow lakes in central China. Our results indicated that the phytoplankton community in the study areas could be mainly classified into 1. Cryptophyta dominated group, 2. Biologically diverse group, and 3. Cyanobacteria dominated group. The Multinomial Logistic Regression model indicated the Cryptophyta dominated group was sensitive to temperature, while other groups were sensitive to both temperature and nutrients. The interactive effects of temperature and nutrients were synergistic in the cyanobacteria dominated group, while they were antagonistic or minor in other groups. The Negative Binomial Regression model suggested high total phosphorus and low total nitrogen but not temperature were responsible for high cyanobacteria abundance. The conditional plot indicated nutrients affected cyanobacteria abundance more significantly under low wind speeds and lake volume fluctuations, and cyanobacteria abundance in the cyanobacteria dominated group maintained high levels with increasing hydrological dynamics. Our results demonstrated that environmental factors played inconsistently significant roles in different phytoplankton groups, and reducing nutrients could decrease adverse effects of warming and water project constructions. Our models can also be applied to forecast phytoplankton shifting and cyanobacteria abundance in the management of regulated shallow lakes.

Environmental antimicrobial resistance and its drivers: a potential threat to public health

Imprudent and overuse of clinically relevant antibiotics in agriculture, veterinary and medical sectors contribute to the global epidemic increase in antimicrobial resistance (AMR). There is a growing concern among researchers and stakeholders that the environment acts as an AMR reservoir and plays a key role in the dissemination of antimicrobial resistance genes (ARGs). Various drivers are contributing factors to the spread of antibiotic-resistant bacteria and their ARGs either directly through antimicrobial drug use in health care, agriculture/livestock and the environment or antibiotic residues released from various domestic settings. Resistant micro-organisms and their resistance genes enter the soil, air, water and sediments through various routes or hotspots such as hospital wastewater, agricultural waste or wastewater treatment plants. Global mitigation strategies primarily involve the identification of high-risk environments that are responsible for the evolution and spread of resistance. Subsequently, AMR transmission is affected by the standards of infection control, sanitation, access to clean water, access to assured quality antimicrobials and diagnostics, travel and migration. This review provides a brief description of AMR as a global concern and the possible contribution of different environmental drivers to the transmission of antibiotic-resistant bacteria or ARGs through various mechanisms. We also aim to highlight the key knowledge gaps that hinder environmental regulators and mitigation strategies in delivering environmental protection against AMR.

Learning from differences: Abiotic determinism of benthic communities in Northern Taiwan

Differences in the initial configuration of ecological communities may lead to contrasting trajectories when facing environmental changes. Here, we propose to uncover the determinism of benthic communities by carrying out a detailed investigation of their response to small-scale modification of environmental conditions, including physical, chemical, and geological factors. At ten locations (confounding site and depth) in Northern Taiwan, communities were delineated using a morpho-functional classification of the organisms. A k-means clustering was used to identify k homogenous groups among transects. Their environmental determinism was examined by combining this result with 16 environmental variables of transect conditions into a regression tree framework. Biotic and abiotic data were further analyzed with a Multivariate Regression Tree (MRT) to ascertain the hierarchical environmental determinism. The classifications produced by both approaches were compared using the Adjusted Rand index (ARI) to assess the predictive power of unsupervised clustering on its missing explanatory components (abiotic variables). k-means and MRT produced five clusters, respectively, with a similarity of 0.82 in ARI. Wave motion, followed by substrate types resolved most of the variance, while chemical factors in this study were uniform throughout the region. Comparable structures for both methods (clustering groups) demonstrated that the delineated clusters matched with contrasting environmental conditions which could be explained by the existence of various benthic communities. Further consideration of these different communities and their environmental context will be important in determining their trajectories under global changes and may help in the interpretation of community modifications with changing environmental conditions.

Only one can remain? Environmental and spatial factors influencing habitat partitioning among invasive and native crayfishes in the Pannonian Ecoregion (Hungary)

Biological invasions have increasingly threatened indigenous species, influence metacommunity organisation and consequently, global biodiversity. World-wide expansion of non-indigenous crayfish (NICS) is associated with dramatic changes in species poor indigenous crayfish (ICS) assemblages challenging conservation planning. We analysed long-term changes of crayfish occurrences from the pre-invasion state, through the first appearance of NICS, to their intensive spread in Hungarian waters. Further, we analysed present-day crayfish metacommunity patterns for co-occurrences and influence of spatial and environmental factors. Historic data revealed a marked pre-invasion decline in indigenous noble crayfish Astacus astacus and stone crayfish Austropotamobius torrentium populations, but not in the narrow-clawed crayfish Pontastacus leptodactylus. Historic data provided no direct evidence for the impact of NICS on ICS, rather it supported that NICS often entered areas where ICS had been extinct or were not present at all. Crayfish species extremely rarely co-occurred which could indicate their strong competition and be related to utilization of empty sites by NICS. Crayfish metacommunities were predominantly spatially structured indicating the primary influence of ongoing invasion. Crayfish species also exhibited different environmental preferences mainly along the altitude and temperature gradients. We conclude that the invasion is still in the expanding phase and without an effective conservational program the future of ICS is doubtful in Hungary. Conservation policy should focus on the preservation and reintroduction of the stone and noble crayfishes in highland refugees. Expansion of NICS should be prevented in refugee areas by utilizing possibilities provided by natural and artificial barriers, and education and strict ban should be simultaneously applied to prevent further illegal releases by aquarists.

Drivers of bacterial diversity along a natural transect from freshwater to saline subtropical wetlands

Tropical coastal wetlands provide a range of ecosystem services that are closely associated with microbially-driven biogeochemical processes. Knowledge of the main players and their drivers in those processes can have huge implications on the carbon and nutrient fluxes in wetland soils, and thus on the ecosystems services we derive from them. Here, we collected surface (0-5 cm) and subsurface (20-25 cm) soil samples along a transect from forested freshwater wetlands, to saltmarsh, and mangroves. For each sample, we measured a range of abiotic properties and characterised the diversity of bacterial communities using 16S rRNA gene amplicon sequencing. The alpha diversity of bacterial communities in mangroves exceeded that of freshwater wetlands, which were dominated by members of the Acidobacteria, Alphaproteobacteria and Verrucomicrobia, and associated with high soil pore-water concentrations of soluble reactive phosphorous, and nitrogen as nitrate and nitrite (N-NO_X^-). Bacterial communities in the saltmarsh were strongly stratified by depth and included members of the Actinobacteria, Chloroflexi, and Deltaproteobacteria. Finally, the mangroves were dominated by representatives of Deltaproteobacteria, mainly Desulfobacteraceae and Synthrophobacteraceae, and were associated with high salinity and soil pore-water concentrations of ammonium (N-NH₄⁺). These communities suggest methane consumption in freshwater wetlands, and sulfate reduction in deep soils of marshes and in mangroves. Our work contributes to the important goal of describing reference conditions for specific wetlands in terms of both bacterial communities and their drivers. This information may be used to monitor change and assess wetland health and function.

Ecological features and global distribution of Asgard archaea

Asgard is a newly proposed archaeal superphylum, which has been suggested to hold the key to decipher the origin of Eukaryotes. However, their ecology remains largely unknown. Here, we conducted a meta-analysis of publicly available Asgard-associated 16S rRNA gene fragments, and found that just three previously proposed clades (Lokiarchaeota, Thorarchaeota, and Asgard clade 4) are widely distributed, whereas the other seven clades (phylum or class level) are restricted to the sediment biosphere. Asgard archaea, especially Loki- and Thorarchaeota, seem to adapt to marine sediments, and water depth (the depth of the sediment below water surface) and salinity might be crucial factors for the proportion of these microorganisms as revealed by multivariate regression analyses. However, the abundance of Asgard archaea exhibited distinct environmental drivers at the clade-level; for instance, the proportion of Asgard clade 4 was higher in less saline environments (salinity <6.35 psu), while higher for Heimdallarchaeota-AAG and Asgard clade 2 in more saline environment (salinity ≥35 psu). Furthermore, co-occurrence analysis allowed us to find a significant non-random association of different Asgard clades with other groups (e.g., Lokiarchaeota with Deltaproteobacteria and Anaerolineae; Odinarchaeota with Bathyarchaeota), suggesting different interaction potentials among these clades. Overall, these findings reveal Asgard archaea as a ubiquitous group worldwide and provide initial insights into their ecological features on a global scale.

Long term effects of fire on the soil greenhouse gas balance of an old-growth temperate rainforest

Forest fires can cause great changes in the composition, structure and functioning of forest ecosystems. We studied the effects of a fire that occurred >50 years ago in a temperate rainforest that caused flooding conditions in a Placic Andosol to evaluate how long these effects last; we hypothesized that the effects of fire on the soil greenhouse gas (GHG) balance could last for many years. We made monthly measurements of fluxes of carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) during two years of soils in an unburned forest (UF) and a nearby site that burned >50 years ago (BS). Our results show that CO₂ emissions from soils were higher in the UF than in the BS, and positively correlated with temperature and negatively with soil water content at both sites. Both sites were net CH₄ sinks (higher in the UF) and fluxes correlated positively with soil water content and negatively with temperature (stronger relation in the BS). Emissions of N₂O were low at both sites and showed correlation with friction velocity at the UF site. The soil GHG balance showed that the UF emitted about 80% more than the BS (5079 ± 1772 and 2815 ± 1447 g CO₂-eq m^-2 y^-1, respectively). Combining our measured fluxes with data of CO₂ net ecosystem exchange, we estimated that at the ecosystem level, the UF was a GHG sink while the BS was a source, showing a long-lasting effect of the fire and the importance of preserving these forest ecosystems.

Statistical approach reveals tidal effect on the antibiotics and environmental relationship with the case study of Yongjiang Estuary, China

We used statistical approach by coupling redundancy analysis with linear regression analysis, which is useful to understand potential sources of antibiotics in the tide rising and ebbing of surface water in the Yongjiang Estuary, China. This study aimed to investigate the relationship between 29 antibiotics at five sites over four seasons and 13 environmental parameters during the tide rising and ebbing durations. The results found that dissolved organic carbon (DOC), salinity, temperature and chlorophyll a (Chla) were the main factors to impact antibiotics. The concentrations of macrolides were increasing with DOC, suggesting DOC may influence the adsorption capacity of antibiotics. The concentrations of tetracyclines had significant correlation with temperature and Chla during the tide rising period. This study demonstrated a method of exploring the relationship between the concentrations of antibiotics and environmental parameters, which is beneficial to future antibiotics research in estuaries.

Dissolved organic carbon and surface active substances in the northern Adriatic Sea: Long-term trends, variability and drivers

The paper presents a unique time series of organic matter content (dissolved organic carbon, DOC, and its surface active substances fraction, SAS) collected in the northern Adriatic along the Po-Rovinj transect between 1998 and 2017. The data were collected on a monthly or bimonthly basis. Seasonal variance of organic matter content does not exceed 30% of its total variance, while the DOC and the SAS trends are significantly negative and positive, respectively, over the whole transect. The organic matter content, however, exhibits pronounced interannual and decadal changes, with periods of high and low carbon content and evident changes in composition of the SAS content. The changes indicate altering episodes between eutrophication and oligotrophication, embedded in the overall oligotrophication trend in the considered period. Both series were correlated with the potential local and regional yearly-averaged drivers in both atmosphere and sea. DOC is most strongly (significant at 99%) correlated with the Po River discharges, at the phase lag of -1 to -2 years. For the SAS, the largest correlations (significant at 99%) are obtained with the Adriatic-Ionian Bimodal Oscillating System index (BiOS index), at the phase lag of -3 to -4 years. Correlations between the organic matter content and the hemispheric or the regional climate indices (North Atlantic Oscillation, East Atlantic/West Russia, East Atlantic, Scandinavian, and Mediterranean Oscillation) are much lower and only sparsely significant at 95% at some phase lags. The same was found for the other local drivers (precipitation and net heat flux). Our analysis highlights the importance of remote processes, like the BiOS, that weren't previously considered to shape the biogeochemical properties of such shallow coastal region impacted by freshwater load. To properly assess such impacts, long-term ecological monitoring and homogenized data series are required.

Suspended particles phoD alkaline phosphatase gene diversity in large shallow eutrophic Lake Taihu

The bacterial phoD gene encodes alkaline phosphatase plays an important role in the release of bioavailable inorganic phosphorus (P) from organic P in environmental systems. However, phoD gene diversity in suspended particles in shallow freshwater lakes is poorly understood. In this study, we explored the potential relationship between environmental factors and phoD phosphatase gene in suspended particles in different ecosystem types (lake zones) in Lake Taihu, a large shallow eutrophic lake in China. Quantitative PCR and high-throughput sequencing were used to analyze phoD gene abundance and the phoD-harboring bacterial community composition. Our results indicate that the distribution of phoD gene abundance in suspended particles had a high spatiotemporal heterogeneity. The phoD gene abundance in each lake zone decreased significantly from June to September. The dominant phoD-harboring phylum in all samples was Actinobacteria, followed by Proteobacteria, Cyanobacteria and Gemmatimonadetes. The first predominant phoD-harboring genera varied among samples, but most of them belonged to phylum Actinobacteria. Driven by different environmental factors, the phoD-harboring bacterial community structure varied with sampling month and ecosystem type. Nitrate and ammonia nitrogen were the main environmental drivers of phoD-harboring bacterial community in suspended particles in the river mouth zone, while water pH and dissolved oxygen were important factors for the algae-dominated, macrophyte-dominated and central lake zones.

Modelling the seasonal impacts of a wastewater treatment plant on water quality in a Mediterranean stream using microbial indicators

Faecal pollution modelling is a valuable tool to evaluate and improve water management strategies, especially in a context of water scarcity. The reduction dynamics of five faecal indicator organisms (E. coli, spores of sulphite-reducing clostridia, somatic coliphages, GA17 bacteriophages and a human-specific Bifidobacterium molecular marker) were assessed in an intermittent Mediterranean stream affected by a wastewater treatment plant (WWTP). Using Bayesian inverse modelling, the decay rates of each indicator were correlated with two environmental drivers (temperature and streamflow downstream of the WWTP) and the generated model was used to evaluate the self-depuration distance (SDD) of the stream. A consistent increase of 1-2 log₁₀ in the concentration of all indicators was detected after the discharge of the WWTP effluent. The decay rates showed seasonal variation, reaching a maximum in the dry season, when SDDs were also shorter and the stream had a higher capacity to self-depurate. High seasonality was observed for all faecal indicators except for the spores of sulphite-reducing clostridia. The maximum SDD ranged from 3 km for the spores of sulphite-reducing clostridia during the dry season and 15 km for the human-specific Bifidobacterium molecular marker during the wet season. The SDD provides a single standardized metric that integrates and compares different contamination indicators. It could be extended to other Mediterranean drainage basins and has the potential to integrate changes in land use and catchment water balance, a feature that will be especially useful in the transient climate conditions expected in the coming years.

N2 fixation in urbanization area rivers: spatial-temporal variations and influencing factors

While nitrogen (N₂) fixation is an important process in nitrogen (N) biogeochemical cycling, supplying a significant portion of the N in natural ecosystems, few quantitative constraints exist concerning its contribution to the N enrichment and export from river ecosystems. This study estimates the N₂ fixation rates of urban rivers in the Yangtze Estuary area using acetylene reduction. The results demonstrate that the prominent spatiotemporal variability of river N₂ fixation rates is driven by various environmental factors. River N₂ fixation rates are significantly higher in the summer (90.57 ± 14.60 ngN·L^-1·h^-1) than in the winter (57.98 ± 15.73 ngN·L^-1·h^-1). Spatially, rivers draining urban and suburban areas have higher N₂ fixation rates than those draining rural areas. The N₂ fixation rates are positively correlated with the N₂ fixing cyanobacteria density, water temperature, light, and the water phosphorus (P) concentration, but they are negatively correlated with the dissolved N concentration (NH₄⁺-N and NO₃^--N). The N₂ fixation rates annually range from 53.20 to 89.24 ngN·L^-1·h^-1 for all of the sampling rivers, which is equivalent to a depth integrated (0-0.6 m) N input of 0.163-0.274 gN·m^-2·a^-1. The determined annual N input via N₂ fixation is generally higher than that of marine systems, but it is lower than that of eutrophic lakes. This study provides robust evidence that N₂ fixation can supply a substantial portion of the N input to human-impacted river ecosystems, which has not been sufficiently accounted for when determining the N mass balance of riverine ecosystems. A high N₂ fixation rate may increase the ratio of N to P input to river systems, and therefore render P the limiting factor in aquatic eutrophication.

Resource availability drives trait composition of butterfly assemblages

How species respond to environmental change is a fundamental question in ecology and species traits can help to tackle this question. In this study, we analyze how the functional structure of species assemblages changes with selected environmental variables along an elevational gradient. In particular, we used species traits of local butterfly communities (body size, voltinism, overwintering stages, and host specificity) in a national nature reserve in China to assess the impacts of temperature, net primary productivity, and land use. Our results show that productivity, measured as NDVI, had a stronger influence on the functional community structure of butterflies than temperature. Within the butterfly assemblages, net primary productivity mainly affected body size and supported few but large species. Length of vegetation period demonstrated dominating effects on the functional structure of local butterfly assemblages. However, an observed increase in dietary generalists with longer vegetation periods contradicted expectations based on niche breadth hypothesis, that more stable conditions should favor specialists. Furthermore, the general positive impact of vegetation period on species abundances differed considerably among functional groups. Only the group containing species hibernating as egg decreased with the length of vegetation period. Our results suggest that trait associations are instructive to explain environment-herbivore relationships, that resource availability can predominantly influence the functional composition of herbivore assemblages, and that conservation priority should be given to specialist butterfly species overwintering as egg, especially in the face of global warming.

Soil microbial biomass: A key soil driver in management of ecosystem functioning

Although patterns of microbial diversity and biomass have been described and reviewed at local and regional scales, a unifying driver, or set of environmental drivers affecting soil microbial biomass (SMB) pattern at global level is still missing. Biomass of soil microbial community, known as SMB is considered widely as the index of soil fertility and ecosystem productivity. The escalating soil stresses due to land degradation and climatic variability are directly correlated with loss of microbial diversity and abundance or biomass dynamics. Therefore, alleviating soil stresses on microbial communities with ecological restoration could reduce the unpredictability and turnover rates of SMB. Thus, the key ecological factors which stabilize the SMB and minimize its turnover, are supposed to play an important role in the soil nutrient dynamics and productivity of the ecosystems. Because of the existing public concern about the deleterious impacts of ecosystem degradation, there is an increasing interest in improving the understanding of SMB, and the way, it contributes to restoration and functioning of ecosystems.

Spouses, social networks and other upstream determinants of type 2 diabetes mellitus

Diabetes risk factors outside the individual are receiving increasing attention. In this issue of Diabetologia, Nielsen et al (DOI: https://doi.org/10.1007/s00125-018-4587-1 ) demonstrate that an individual's obesity level is associated with incident type 2 diabetes in their spouse. This is in line with studies providing evidence for spousal and peer similarities in lifestyle behaviours and obesity. Non-random mating and convergence over time are two explanations for this phenomenon, but shared exposure to more upstream drivers of diabetes may also play a role. From a systems-science perspective, these mechanisms are likely to occur simultaneously and interactively as part of a complex system. In this commentary, we provide an overview of the wider system-level factors that contribute to type 2 diabetes.

Effect of anthropogenic factors, landscape structure, land relief, soil and climate on risk of alien plant invasion at regional scale

We compared the effectiveness of explanatory variables representing different environmental spheres on the risk of alien plant invasion. Using boosted regression trees (BRT), we assessed the effect of anthropogenic factors, soil variables, land relief, climate and landscape structure on neophyte richness (NR) (alien plant species introduced after the 15th century). Data on NR were derived from a 2 × 2 km grid covering a total area of 31,200 km² of the Carpathian massif and its foreground, Central Europe. Each of the examined environmental spheres explained NR, but their explanatory ability varied more than two-folds. Climatic variables explained the highest fraction of deviation, followed by anthropogenic factors, soil type, land relief and landscape structure. The global model, which incorporated crucial variables from all studied environmental spheres, had the best explanatory ability. However, the explained deviation was far smaller than the sum of the deviations explained by the single-sphere models. The global model showed that the deviation that could be explained by variables representing particular spheres, overlapped. The variables representing landscape structure were not included in the global model as they were found to be redundant. Finally, the climatic variables explained a smaller fraction of the deviation than the anthropogenic factors. The partial dependency plots allowed the assessment of the course of dependencies between NR and particular explanatory variables after eliminating the average effect of all other variables. The relationships were usually curvilinear and revealed some values of environmental variables beyond which NR changed considerably.

Environmental variables associated with anopheline larvae distribution and abundance in Yanomami villages within unaltered areas of the Brazilian Amazon

Background

Many indigenous villages in the Amazon basin still suffer from a high malaria burden. Despite this health situation, there are few studies on the bionomics of anopheline larvae in such areas. This publication aims to identify the main larval habitats of the most abundant anopheline species and to assess their associations with some environmental factors.

Methods

We conducted a 19-month longitudinal study from January 2013 to July 2014, sampling anopheline larvae in two indigenous Yanomami communities, comprised of four villages each. All natural larval habitats were surveyed every two months with a 350 ml manual dipper, following a standardized larval sampling methodology. In a third study area, we conducted two field expeditions in 2013 followed by four systematic collections during the long dry season of 2014–2015.

Results

We identified 177 larval habitats in the three study areas, from which 9122 larvae belonging to 13 species were collected. Although species abundance differed between villages, An. oswaldoi (s.l.) was overall the most abundant species. Anopheles darlingi, An. oswaldoi (s.l.), An. triannulatus (s.s.) and An. mattogrossensis were primarily found in larval habitats that were partially or mostly sun-exposed. In contrast, An. costai-like and An. guarao-like mosquitoes were found in more shaded aquatic habitats. Anopheles darlingi was significantly associated with proximity to human habitations and larval habitats associated with river flood pulses and clear water.

Conclusions

This study of anopheline larvae in the Brazilian Yanomami area detected high heterogeneities at micro-scale levels regarding species occurrence and densities. Sun exposure was a major modulator of anopheline occurrence, particularly for An. darlingi. Lakes associated with the rivers, and particularly oxbow lakes, were the main larval habitats for An. darlingi and other secondary malaria vectors. The results of this study will serve as a basis to plan larval source management activities in remote indigenous communities of the Amazon, particularly for those located within low-order river-floodplain systems.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2517-6) contains supplementary material, which is available to authorized users.

Environmental drivers that influence microalgal species in fullscale wastewater treatment high rate algal ponds

In the last decade, studies have focused on identifying the most suitable microalgal species for coupled high rate algal pond (HRAP) wastewater treatment and resource recovery. However, one of the challenges facing outdoor HRAP systems is maintaining microalgal species dominance. By increasing our understanding of the environmental drivers of microalgal community composition within the HRAP environment, it may be possible to manipulate the system in such a way to favour the growth of desirable species. In this paper, we investigate the microalgal community composition in two full-scale HRAPs over a 23-month period. We compare wastewater treatment performance between dominant species and identify the environmental drivers that trigger change in community composition. A total of 33 microalgal species were identified over the 23-month period but species richness (the number of species present at any given time) was low and was not related to either productivity or nutrient removal efficiency. Species turnover of the dominant microalgae happened rapidly, typically <1 week. Changes in the influent NH₄-N concentration and zooplankton grazer numbers were significantly associated with species turnover, accounting for 80% of the changes in dominant species throughout the 23-month study period. Both nutrient removal and biomass production did not differ between the two HRAPs when the dominant species was the same or differed in the two ponds. These results suggest that microalgal functional groups are more important than individual species for full-scale HRAP performance. This study has increased our understanding of some of the environmental drivers of the microalgae within the HRAP environment, which may assist with improving wastewater treatment and resource recovery.

Variation in the health and biochemical condition of the coral Acropora tenuis along two water quality gradients on the Great Barrier Reef, Australia

This study explores how plasticity in biochemical attributes, used as indicators of health and condition, enables the coral Acropora tenuis to respond to differing water quality regimes in inshore regions of the Great Barrier Reef. Health attributes were monitored along a strong and weak water quality gradient, each with three reefs at increasing distances from a major river source. Attributes differed significantly only along the strong gradient; corals grew fastest, had the least dense skeletons, highest symbiont densities and highest lipid concentrations closest to the river mouth, where water quality was poorest. High nutrient and particulate loads were only detrimental to skeletal density, which decreased as linear extension increased, highlighting a trade-off. Our study underscores the importance of assessing multiple health attributes in coral reef monitoring. For example, autotrophic indices are poor indicators of coral health and condition, but improve when combined with attributes like lipid content and biomass.

Effects of temperature, salinity and composition of the dinoflagellate assemblage on the growth of Gambierdiscus carpenteri isolated from the Great Barrier Reef

Increases in reported incidence of ciguatera fish poisoning (hereafter ciguatera) have been linked to warmer sea temperatures that are known to trigger coral bleaching events. The drivers that trigger blooms of ciguatera-causing dinoflagellates on the Great Barrier Reef (GBR) are poorly understood. This study investigated the effects of increased temperatures and lowered salinities, often associated with environmental disturbance events, on the population growth of two strains of the potentially ciguatera-causing dinoflagellate, Gambierdiscus carpenteri (NQAIF116 and NQAIF380). Both strains were isolated from the central GBR with NQAIF116 being an inshore strain and NQAIF380 an isolate from a stable environment of a large coral reef aquarium exhibit in ReefHQ, Townsville, Australia. Species of Gambierdiscus are often found as part of a mixed assemblage of benthic toxic dinoflagellates on macroalgal substrates. The effect of assemblage structure of dinoflagellates on the growth of Gambierdiscus populations has, however, not been explored. The study, therefore investigated the growth of G. carpenteri within mixed assemblages of benthic dinoflagellates. Population growth was monitored over a period of 28days under three salinities (16, 26 and 36) and three temperature (24, 28 and 34°C) conditions in a fully crossed experimental design. Temperature and salinity had a significant effect on population growth. Strain NQAIF380 exhibited significantly higher growth at 28°C compared to strain NQAIF116, which had highest growth at 24°C. When strain NQAIF116 was co-cultured with the benthic dinoflagellates, Prorocentrum lima and Ostreopsis sp., inhibitory effects on population growth were observed at a salinity of 36. In contrast, growth stimulation of G. carpenteri (strain NQAIF116) was observed at a salinity of 26 and particularly at 16 when co-cultured with Ostreopsis-dominated assemblages. Range expansion of ciguatera-causing dinoflagellates could lead to higher frequency of reported ciguatera illness in populated temperate Australian regions, outside the tropical range of the GBR. Therefore, the findings on salinity and temperature tolerance of two strains of G. carpenteri indicates potential adaptability to different local environmental conditions. These are baseline data for future investigations into the potential southward range expansion of ciguatera-causing dinoflagellates originating from the GBR.

Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem

Microbial symbionts inhabit tissues of all plants and animals. Their community composition depends largely on two ecological processes: (1) filtering by abiotic conditions and host species determining the environments that symbionts are able to colonize and (2) dispersal-limitation determining the pool of symbionts available to colonize a given host and community spatial structure. In plants, the above- and belowground tissues represent such distinct habitats for symbionts that we expect different effects of filtering and spatial structuring on their symbiont communities. In this study, we characterized above- and belowground communities of fungal endophytes--fungi living asymptomatically within plants--to understand the contributions of filtering and spatial structure to endophyte community composition. We used a culture-based approach to characterize endophytes growing in leaves and roots of three species of coastal beachgrasses in dunes of the USA Pacific Northwest. For leaves, endophyte isolation frequency and OTU richness depended primarily on plant host species. In comparison, for roots, both isolation frequency and OTU richness increased from the nutrient-poor front of the dune to the higher-nutrient backdune. Endophyte community composition in leaves exhibited a distance-decay relationship across the region. In a laboratory assay, faster growth rates and lower spore production were more often associated with leaf- than root-inhabiting endophytes. Overall, our results reveal a greater importance of biotic filtering by host species and dispersal-limitation over regional geographic distances for aboveground leaf endophyte communities and stronger effects of abiotic environmental filtering and locally patchy distributions for belowground root endophyte communities.

Three decades of sea water abstraction by Kapar power plant (Malaysia): What impacts on tropical zooplankton community?

Zooplankton samples collected before (1985-86) and after (2013-14) the establishment of Kapar power station (KPS) were examined to test the hypothesis that increased sea surface temperature (SST) and other water quality changes have altered the zooplankton community structure. Elevated SST and reduced pH were detected between before and after impact pairs, with the greatest impact at the station closest to KPS. Present PAHs and heavy metal concentrations are unlikely causal factors. Water parameter changes did not affect diversity but community structure of the zooplankton. Tolerant small crustaceans, salps and larvaceans likely benefited from elevated temperature, reduced pH and shift to a more significant microbial loop exacerbated by eutrophication, while large crustaceans were more vulnerable to such changes. It is predicted that any further rise in SST will remove more large-bodied crustacean zooplankton, the preferred food for fish larvae and other meroplankton, with grave consequences to fishery production.

On the distribution and population dynamics of the ctenophore Mnemiopsis leidyi in the Belgian part of the North Sea and Westerschelde estuary

The spatio-temporal distribution and population dynamics of the non-indigenous ctenophore Mnemiopsis leidyi A. Agassiz 1865 were investigated through monthly and quarterly surveys in 2011-2012 at several locations in the Belgian part of the North Sea, the main coastal ports and the adjacent Westerschelde estuary. M. leidyi occurred from August to December, but was never found more than 30 km offshore. Densities were generally low (average 0.8 ± SD 2.8 ind m(-3)) compared to other invaded European systems. Highest densities of M. leidyi were found in the semi-enclosed basin (port of Oostende; 18.4 ind m(-3)) and Westerschelde estuary (1.9 ind m(-3)). The presence of larvae and sudden appearance of high numbers across the size distribution in August indicated that ports and estuaries may act as sources, populating the adjacent coastal area. The zero-inflated logistic regression model showed that there is a higher chance of finding M. leidyi (presence) when temperature declines from late summer onwards. Combined with a negative binomial regression, our model suggests that increasing M. leidyi densities are associated with decreasing autumn temperatures, low wave height (low energetic systems) and low dissolved oxygen concentrations Although densities remained relatively low since its first appearance in 2007, a permanent population seems to be established in Belgian waters. As population outbursts may occur with only a small change in environmental parameters, further monitoring of this notorious invasive species is recommended.