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Agricultural drainage ditches (ADDs) are ubiquitous and regarded as active zones for biogeochemical reactions and microbe-mediated pollutant removal. However, little is known about the microbial distribution and community assembly in ADDs. Here, a typical large-scale irrigation district, including five orders of farmland drainage systems (namely field, sublateral, head, branch, and trunk ditches that could efficiently remove excess water from paddy fields to downstream water bodies), was selected to investigate the ecological processes of microbial communities and N- and P-transformation processes in multistage ditches. We found that scale effects drove distinct environmental gradients and microbial community dissimilarities and that the five ordered ditches were grouped into three clusters (field vs. sublateral vs. head, branch, and trunk ditches). Specifically, the microbial communities in the field ditches located adjacent to the paddy fields were strongly selected by agricultural fertilization and irrigation drainage, enriching salt-tolerant microbes with high nitrification and inorganic P solubilization capabilities. In comparison, the sublateral ditches showed the highest removal performance for total nitrogen (13.28–55.80%) and total phosphorus (9.06–65.07%) during the growth of rice, which was mainly attributed to the enrichment of versatile microbiota (e.g., C39 , Nitrospira, and Novosphingobium) as a result of the increased stochastic processes driven by the low redox potential. Notably, the specific gene (i.e., hzsB) for anaerobic ammonium oxidation in sublateral ditches was 1–2 orders of magnitude higher than in adjacent ditches, further contributing to N loss. As field water was discharged into the large-sized head, branch, and trunk ditches, the nutrient levels decreased sharply. At the same time, deterministic processes gained more importance (∼82%), leading to the flourishing of Synechococcus and increasing the potential risk of eutrophication. Overall, the microbial communities in multistage ADDs were co-shaped by agricultural practices and ditch size, which further governed the N and P removal performance. These results provide unique insights into microbiota assembly patterns and dynamics in multistage ADDs and important ecological knowledge for controlling agricultural non-point source pollutants by managing of small-sized ditches. [Display omitted] • Microbial dynamics and their contributions to N and P removal were investigated. • Microbial communities in multistage drainage ditches were scale dependent. • Agricultural practices and ditch size co-shape the microbial communities in ditches. • Local heterogeneity enhanced stochastic process and enriched functional microbiota. • Multistage drainage ditches were efficient to control non-point source pollutants. [ABSTRACT FROM AUTHOR]

River-reservoir systems have become ubiquitous among modern global aquatic environments due to the widespread construction of dams. However, little is known of antibiotic resistance gene (ARG) distributions in reservoir-river systems experiencing varying degrees of anthropogenic impacts. Here, the diversity, abundance, and spatial distribution of ARGs were comprehensively characterized along the main stem of the Minjiang River, a typical subtropic reservoir-river system in Southeast China using high-throughput quantitative PCR. A total of 252 ARG subtypes were detected from twelve sampling sites that were dominated by aac(3)-Via , followed by czcA , blaTEM , and sul1. Urban river waters (sites S9–S12) harbored more diverse ARGs than did the reservoir waters (sites S1–S7), indicating more serious antibiotic resistance pollution in areas with larger population densities. Dam construction could reduce the richness and absolute abundance of ARGs from upstream (site S7) to downstream (site S8). Urban river waters also harbored a higher proportion of mobile genetic elements (MGEs), suggesting that intensive human activities may promote ARG horizontal gene transfers. The mean relative abundance of Proteobacteria that could promote antibiotic resistance within microbial communities was also highest in urban river waters. Variance partitioning analysis indicated that MGEs and bacterial communities could explain 67.33%, 44.7%, and 90.29% of variation in selected ARGs for the entire watershed, aquaculture waters, and urban river waters, respectively. These results further suggest that urban rivers are ideal media for the acquisition and spread of ARGs. These findings provide new insights into the occurrence and potential mechanisms determining the distributions of ARGs in a reservoir-river system experiencing various anthropogenic disturbances at the watershed scale. [Display omitted] • HT-qPCR was used for characterization of ARG and MGE profiles. • Urbanized river sites harbored more diverse ARGs than did the reservoir waters. • Dam construction could reduce the transport of ARGs from upstream to downstream. • MGEs and bacterial community explained 90.30% of ARG variations in the urban sites. [ABSTRACT FROM AUTHOR]

Microbial communities are important elements in the marine environment, contributing to nutrient cycling and biogeochemical processes. Estuaries comprise environments exhibiting characteristics from freshwater to marine, leading to distinct microbial communities across this environmental gradient. Here, we examine the spatial dynamics of microbial communities in Macquarie Harbour, an estuarine system on the West coast of Tasmania, Australia. Water was sampled along the estuary to explore the structure and composition of the microbial communities using 16S/18S rRNA gene amplicon sequencing. Multivariate analyses showed environmental variables and community compositions varying along a longitudinal (river to adjacent ocean) gradient at the surface. In the Harbour, differences in the microbial community were observed between surface (0–1 m) and intermediate depths (4.5–11 m depth). The results of differential abundance, network and Partial Least Square analyses suggest that Macquarie Harbour is a mixing zone, where the distributions of archaeal, bacterial and eukaryotic communities are influenced by oceanic and riverine inputs. These results provide critical insights into the Macquarie Harbour environment and the importance of understanding the role of microbial communities for similar systems elsewhere. • Network and machine learning revealed the microbial community structure in a highly stratified aquatic environment. • Environmental variables and community compositions varied along a longitudinal (river to adjacent ocean) gradient. • Oceanic and riverine inputs contribute to differences in the composition of microbial communities. • Pelagic heterotrophic microorganisms may play important roles in the nutrient cycle in the Macquarie Harbour. [ABSTRACT FROM AUTHOR]

Predicting responses of plant communities to environmental changes is a key challenge in ecology. Here we examined climate-related mechanisms regulating seedling dynamics of a common Mediterranean shrub. Our objective was to analyze effects of water availability on seedling survival and to determine whether geographical gradients can serve as proxy for predicting local climate change effects. We conducted a field experiment along a natural rainfall gradient with additional long-term rainfall manipulations at a Mediterranean site, enabling the investigation of the relative importance of biotic and abiotic factors on seedling dynamics. Along the natural and artificial rainfall gradient seedling survival increased with increasing soil water availability. However, seedling survival at the Mediterranean site yielded a clear trend of decreasing seedling survival with artificially increasing aridity whereas at the dry end of the geographical gradient seedling survival was relatively high. We attribute this pattern to biotic interactions, which appeared less negative at the dry end. These findings indicate that ignoring biotic interactions is misleading when predicting shifts in the distribution of species under climate change and that because of the complex interplay between abiotic and biotic factors, environmental gradients can be poor proxies for predicting the response of plant species to climate change. [ABSTRACT FROM AUTHOR]

Abstract: The climatic controls on decomposition rates have gained considerable interest in recent years because of a perceived risk that elevated global temperatures could lead to positive green house gas feedbacks from soil ecosystems. Previous relationships between decomposition rates and abiotic variables like temperature and moisture have been proved confounding, particularly for dryland ecosystems. Decomposition rates of two grass species, Pseudoroegneria spicata (Pursh) Á. Löve and Calamagrostis rubescens Buckley, which represent dominant understory cover at either end of a semi-arid grassland to forest ecocline near Kamloops, British Columbia, Canada, were measured. Despite differences in %N and C:N, decomposition rates between the two species were similar. Elevation was strongly correlated with rate of decomposition for both species. We provide evidence of a positive correlation of water availability and a negative correlation of temperature on decomposition rates along the elevational ecocline. Decomposition rates were higher during the wetter spring period than during summer, at higher elevations and in more mesic ecosystems. We found no ‘home-field’ advantage for P. spicata and C. rubescens on decomposition rates. Our results provide evidence that available moisture is an important control on decomposition rates in dryland ecosystems. [Copyright &y& Elsevier]

Abstract: The potential impact of climate change on biodiversity is well documented. A well developed range of statistical methods currently exists that projects the possible future habitat of a species directly from the current climate and a species distribution. However, studies incorporating ecological and evolutionary processes remain limited. Here, we focus on the potential role that local adaptation to climate may play in driving the range dynamics of sessile organisms. Incorporating environmental adaptation into a stochastic simulation yields several new insights. Counter-intuitively, our simulation results suggest that species with broader ranges are not necessarily more robust to climate change. Instead, species with broader ranges can be more susceptible to extinction as locally adapted genotypes are often blocked from range shifting by the presence of cooler adapted genotypes that persist even when their optimum climate has left them behind. Interestingly, our results also suggest that it will not always be the cold-adapted phenotypes that drive polewards range expansion. Instead, range shifts may be driven by phenotypes conferring adaptation to conditions prevalent towards the centre of a species’ equilibrium distribution. This may have important consequences for the conservation method termed predictive provenancing. These initial results highlight the potential importance of local adaptation in determining how species will respond to climate change and we argue that this is an area requiring urgent theoretical and empirical attention. [ABSTRACT FROM AUTHOR]

Abstract: We compared physiological and morphological traits of Thymus loscosii, a rare endemic of semiarid Spain, and Thymus vulgaris, a widespread Mediterranean species, over a precipitation gradient, and measured the spatial patterns of both species. Our results do not provide evidence for a congruent suite of traits associated with rarity in T. loscosii, since this species showed some traits reported in rare species (lower height and biomass), but exhibited better performance under severe climatic conditions (higher photochemical efficiency and quantum yield during winter) and higher values of traits conferring competitive abilities (SLA and LAR). T. loscosii did not show either lower phenotypic variability or better performance than its congener along the precipitation gradient. The two thymes were spatially dissociated when they co-occurred and the spatial pattern of T. loscosii changed from clumped in the presence of its congener to random when it was the only thyme, suggesting competition between the two species. These results suggest that T. loscosii is not a habitat-specialist and may behave as a refuge endemic. Its reduced distribution may be linked to a limited competitive ability that is not associated with the vegetative traits explored, although other causes like habitat degradation and genetic or reproductive constraints might also be important to explain its limited distribution. [Copyright &y& Elsevier]

Abstract: The South American cordgrass, Spartina densiflora, has invaded a range of different habitats that can support different native species assemblages on salt marshes in the Gulf of Cadiz, Spain. Little is known about the mechanisms of invasion. We examined the potential for seed germination and recruitment in a field transplant experiment, representing a wide range of environments, on elevational gradients across marshes with muddy and sandy sediments. The biotic resistance of native, perennial vegetation (where present) to recruitment of the alien was also investigated. Spartina densiflora seeds were able to germinate over a greater than 2-m range of elevation in the tidal frame. Germination success on unvegetated muddy sediments was related to sediment redox potential, with poor germination at strongly negative redox potentials on the lower sites. On sandy, well-drained sediments, germination was apparently constrained by water availability at the highest elevations. Comparison of vegetated and cleared plots on the upper marsh showed that there was a negative relationship between the presence of Atriplex portulacoides and germination on the muddy sediments. Recruitment (survival of seedlings for 12weeks) was seen only on unvegetated muddy sediments at the highest elevation. Hence the invasive success and wide elevational tolerance of S. densiflora on the marshes of the Gulf of Cadiz are not reflected in its short-term ability to become established from its prolific seed production. Colonization of sub-optimal habitats may be largely by vegetative propagules and clonal growth. [Copyright &y& Elsevier]

Coastal habitats are critical transition zones supporting a diverse and abundant marine community but are under strong human influence. Sustainable management of those habitats must rely on robust understanding of the processes regulating the diversity and functioning of the local communities. However, most of the studies to date have focused predominantly on the benthic communities from positive surface of rocks. Here, using a sessile community from negative surfaces, we described how larval availability, recruitment, predation and physical parameters affect the diversity and distribution of species along a gradient formed from the mouth to the middle portions of a diverse coastal bay threatened by the expansion of a port in the Southwestern Atlantic Ocean. Monthly, from August 2015 to November 2016, we compared the composition of sessile species on the lateral and undersurface of rocks, the water physical parameters, the substrate composition and availability, as well as the abundance of larvae in the plankton and the recruitment in the mouth and the middle portions of the bay. Additionally, we also conducted a predator exclusion experiment to compare the predation pressure across the bay. The sessile community in the middle of the bay is a subset of the community in the mouth, where ascidians and bryozoans contributed to increase diversity. While the amount of rocky substrate was similar between sites, the proportion of granite, the water turbidity and the chlorophyll concentration were higher in the middle of the bay. Larvae and recruits were more abundant in the middle of the bay, mainly during the spring and summer months, but recruits were more diverse in the mouth of the bay during the whole study. Although reducing diversity, predation had similar effects in the two sites and did not explain the differences in the sessile communities. Our results reinforce that in critical transition zones, the relative importance of regional oceanic and local processes changes along the ocean-land gradient. While communities in the mouth of the bay are more diverse and dynamic, being composed by several species of colonial filter-feeding organisms, the high turbidity in the middle of the bay seems to restrict those organisms, resulting in communities mainly composed by serpulid worms and oysters. Communities closer to the bottom of the bay are also near to the source of allochthonous sediments and nutrients, being consequently more susceptible to human disturbances. [Display omitted] • Composition of cryptic communities differs across a small-scale ocean-land gradient. • Outer regions of the bay support more diverse recruits and communities. • Predation reduces overall recruitment and species richness by removing rare species. • Local and regional processes regulate cryptic community in critical transition zones. [ABSTRACT FROM AUTHOR]

Abstract: This study analyzed the factors structuring demersal fish community in a tropical bay in southeastern Brazil. The results were used to quantify the partitioning of ecological variation among the environmental, spatial and temporal components molding the fish community. Three bay zones (inner, middle and outer) were defined according to depth and salinity gradient. Monthly samplings were conducted by bottom trawl tows during daylight hours, between October 1998 and September 1999. In each zone, three replicate samples were taken. Ninety-three fish species from 73 genera and 37 families were recorded in the 108 samples. Two demersal fish assemblages were evidenced, one in the inner and the other in the outer zone. These assemblages were characterized by changes in species composition and relative abundance. Depth, followed by transparency and salinity, influenced spatial pattern of fish assemblages. The largest part of the explained variation occurred as a result of the spatial structure of environmental variables, which means that both species and environmental variables presented similar spatial structure. The spatial effect, not the seasonal, explained the highest part of species variations. The amount of unexplained variation was relatively high (76%), even assuming that part of it is due to nondeterministic fluctuation, which could be due to local effects of unmeasured (biotic and abiotic) controlling variables. Knowing the relative importance of these factors can be of decisive importance when applying casual hypotheses in the framework of some precise ecological theory and should facilitate management, planning, and usage of bay resources. [Copyright &y& Elsevier]

Abstract: Estuaries, lagoons and mudflat habitats represent a crucial biodiversity component in coastal waters and may act as vital nurseries and shelters for the juvenile stages of many commercial fish species. A study of the spatial distribution of inshore fish fauna around the shallow coastal habitats of North Bull Island (Dublin Bay, Ireland) was carried out during summer and autumn of 2005, in order to characterise the fish community present therein. Four stations were examined, situated along a putative environmental gradient, between the mudflat and the open sea shore. Stations were surveyed at both high and low tide and sampling was repeated weekly for eight weeks, spanning over four spring and four neap tidal events. A total of 17 fish species were caught, belonging to 13 families. The community was largely dominated by the lesser sandeel (Ammodytes tobianus) and the common goby (Pomatoschistus microps). Ordination techniques were used to generate hypotheses as to the general patterns in the fish community; Shannon–Wiener index was employed to estimate spatial, temporal and tidal trends in diversity; and analysis of variance (ANOVA) was employed to test for the influence of time of the year, habitat, tidal phase and tidal state on the spatial distribution of fishes. Results reveal that time of the year and habitat variation across the environmental gradient are the major factors in determining fish community structure. The influence of tidal dynamics seem to have a lesser impact on the overall community, but can significantly and variably affect the distribution of individual species. [Copyright &y& Elsevier]

Abstract: Spatial variation of water column characteristics, sediment parameters and irradiance on coral reefs was examined in the Whitsunday region of the Great Barrier Reef during five sampling events between 2004 and 2006. Sampling locations were selected along a transect from outer reefs distant from terrestrial inputs, to coastal reefs near the Australian mainland. Most of the water column variables (especially chlorophyll a, total suspended solids, particulate organic carbon and particulate nutrients) and irradiance variables (Secchi and optical depth) changed significantly along the transect. For example, concentrations of chlorophyll a and total suspended solids increased two- and three-fold, respectively, from outer to coastal locations, while sediment inorganic carbon decreased and sediment colour became darker. Similarly, Secchi and optical depth, two measures of water transparency, decreased approximately three-fold towards the coast. Most of these gradients were persistent over the five sampling events, but for several parameters, the magnitude and steepness of the gradient changed. The maximum depth of zooxanthellate corals decreased five-fold along the gradient from outer to coastal locations and was related significantly to a water quality index derived for the Whitsunday Islands. Our data of the maximal depth limit for reef development at locations where suitable settlement substrata were available suggest that the absolute minimum of light required for a reef to persist is in the range of 6–8% of surface irradiance in the Whitsunday Islands. [Copyright &y& Elsevier]

Fish and macrocrustacean assemblage structure was analyzed along an estuarine gradient at Mad Island Marsh (MIM), Matagorda Bay, TX, during March 1998–August 1999. Eight estuarine-dependent fish species accounted for 94% of the individual fishes collected, and three species accounted for 96% of macrocrustacean abundance. Consistent with evidence from other Gulf of Mexico estuarine studies, species richness and abundance were highest during late spring and summer, and lowest during winter and early spring. Sites near the bay supported the most individuals and species. Associations between fish abundance and environmental variables were examined with canonical correspondence analysis. The dominant gradient was associated with water depth and distance from the bay. The secondary gradient reflected seasonal variation and was associated with temperature, salinity, dissolved oxygen, and vegetation cover. At the scales examined, estuarine biota responded to seasonal variation more than spatial variation. Estuarine-dependent species dominated the fauna and were common throughout the open waters of the shallow lake during winter–early spring when water temperature and salinity were low and dissolved oxygen high. During summer–early fall, sub-optimal environmental conditions (high temperature, low DO) in upper reaches accounted for strong spatial variation in assemblage composition. Small estuarine-resident fishes and the blue crab (Callinectes sapidus) were common in warm, shallow, vegetated inland sites during summer–fall. Estuarine-dependent species were common at deeper, more saline locations near the bay during this period. During summer, freshwater species, such as gizzard shad (Dorosoma cepedianum) and gars (Lepisosteus spp.), were positively associated with water depth and proximity to the bay. The distribution and abundance of fishes in MIM appear to result from the combined effects of endogenous, seasonal patterns of reproduction and migration operating on large spatial scales, and species-specific response to local environmental variation. [Copyright &y& Elsevier]