Core community drives phyllosphere bacterial diversity and function in multiple ecosystems

The phyllosphere provides a habitat for a large sum of microorganisms which are modulated by numerous biotic and abiotic factors. While it is logical that host lineage must have some effect on the phyllosphere habitat, it is unclear if phyllospheres harbor similar microbial core communities across multiple ecosystems at the continental-scale. Here we collected 287 phyllosphere bacterial communities from seven ecosystems (including paddy field, dryland, urban area, protected agricultural land, forest, wetland, and grassland) in east-China to identify the regional core community and to characterize the importance of such communities in maintaining phyllosphere bacterial community structure and function. Despite significantly different bacterial richness and structure, the seven studied ecosystems contained a similar regional core community of 29 OTUs that comprised 44.9 % of the total bacterial abundance. The regional core community was less affected by environmental variables and less connected in the co-occurrence network compared with other non-core OTUs (the whole minus regional core community). Furthermore, the regional core community also had a large proportion (>50 %) of a constrained set of nutrient metabolism related functional potentials and less functional redundancy. This study suggests there is a robust regional core phyllosphere community regardless of ecosystem or spatial and environmental heterogeneity, and supports the argument that core communities are pivotal in maintaining microbial community structure and function.

Characterizing sediment functional traits and ecological consequences respond to increasing antibiotic pollution

Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. KEY POINTS: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH₄ efflux, while mitigating N₂O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations.

Responses of macroinvertebrate functional trait structure to river damming: From within-river to basin-scale patterns

Revealing how aquatic organisms respond to dam impacts is essential for river biomonitoring and management. Traditional examinations of dam impacts on macroinvertebrate assemblages were frequently conducted within single rivers (i.e., between upstream vs. downstream locations) and based on taxonomic identities but have rarely been expanded to level of entire basins (i.e., between dammed vs. undammed rivers) and from a functional trait perspective. Here, we evaluated the effects of dams on macroinvertebrate assemblages at both the within-river and basin scales using functional traits in two comparable tropical tributaries of the Lancang-Mekong River. At different scales, maximum body size, functional feeding groups (FFG), voltinism and occurrence in drift respond significantly to dam impact. Armoring categories varied significantly between downstream sites and upstream sites, and oviposition behavior, habits and adult life span significantly differed between rivers. The key traits at the within-river scale resembled to those at the between-river scale, suggesting that within-river trait variation could further shape functional trait structure at the basin scale in dammed rivers. Furthermore, water nutrients and habitat quality induced by dams showed the most important role in shaping trait structure, although trait-environment relationships varied between the two different scales. In addition, the trait-environment relationships were stronger in the dry season than in the wet season, suggesting a more important role of environmental filtering processes in the dry season compared with the wet season. This study highlights the utility of the trait-based approach to diagnose the effects of damming and emphasizes the importance of spatial scale to examine dam impacts in riverine systems.

Functional structure mediates the responses of productivity to addition of three nitrogen compounds in a meadow steppe

Atmospheric nitrogen (N) deposition is altering grassland productivity and community structure worldwide. Deposited N comes in different forms, which can have different consequences for productivity due to differences in their fertilization and acidification effects. We hypothesize that these effects may be mediated by changes in plant functional traits. We investigated the responses of aboveground primary productivity and community functional composition to addition of three nitrogen compounds (NH₄NO₃, [NH₄]₂SO₄, and CO[NH₂]₂) at the rates of 0, 5, 10, 20 g N m^-2 yr^-1. We used structural equation modeling (SEM) to evaluate how functional structure influences the responses of productivity to the three N compounds. Nitrogen addition increased community-level leaf chlorophyll content but decreased leaf dry matter content and phosphorus concentration. These changes were mainly due to intra-specific variation. Functional dispersion of traits was reduced by N addition through changes in species composition. SEM revealed that fertilization effects were more important than soil acidification for the responses of productivity to CO(NH₂)₂ addition, which enhanced productivity by decreasing functional trait dispersion. In contrast, the effects of (NH₄)₂SO₄ and NH₄NO₃ were primarily due to soil acidification, influencing productivity via community-weighted means of functional traits. Our results suggest that N forms with different fertilizing and acidifying effects influence productivity via different functional traits pathways. Our study also emphasizes the need for in situ experiments with the relevant N compounds to accurately understand and predict the ecological effects of atmospheric N deposition on ecosystems.

Effect of multiple stressors on the functional traits of sub-tidal macrobenthic fauna: A case study of the southeast coast of India

The use of functional information of taxa is a promising approach to uncover the underlying mechanism of ecosystem functioning. We used biological trait analysis (BTA) to assess the functional response of subtidal macrobenthos with multiple stressors. Seventeen environmental variables from 42 stations of five coastal districts were assessed along the southeast coast of India. Dominant fauna was assigned into 20 categories belonging to six functional traits. Additionally, we used five ecological groups (EG) of AMBI as a covariable trait to validate functional traits and EG relationship. The trait composition in the communities showed significant variation between undisturbed and disturbed areas. RLQ/Fourth corner combined approach illustrated the effects of stressors and isolated the corresponding species associated with different stressors. Smaller, short-lived, deposit-feeding, and discretely motile fauna occurred at the disturbed areas, whereas, larger, long-lived, and highly motile at the undisturbed area. Dissolved oxygen, organic enrichment, and metals concentration were the main environmental descriptors influencing the trait composition. The results highlight the importance of the BTA approach to uncover the response of the macrobenthic community to anthropogenic disturbances-driven impacts in multi-stressed near-shore coastal ecosystems.

Greater functional similarity in mobile compared to sessile assemblages colonizing artificial coastal habitats

Among anthropogenic habitats built in the marine environment, floating and non-floating structures can be colonized by distinct assemblages. However, there is little knowledge whether these differences are also reflected in the functional structure. This study compared the functional diversity of sessile and mobile invertebrate assemblages that settle over three months on floating vs. non-floating artificial habitats, in two Chilean ports. Using morphological, trophic, behavioral, and life history traits, we found differences between mobile and sessile assemblages regarding the effect of the type of habitat on the functional diversity. Compared to sessile assemblages, a greater functional similarity was observed for mobile assemblages, which suggests that their dispersal capacity enables them to balance the reduced connectivity between settlement structures. No traits, prevailing or selected in one or the other habitat type, was however clearly identified; a result warranting for further studies focusing on more advanced stages of community development.

Phylogenetic and functional structures of succession in plant communities on mounds of Marmota himalayana in alpine regions on the northeast edge of the Qinghai-Tibet Plateau

Few studies have examined the succession of plant communities in the alpine zone. Studying the succession of plant communities is helpful to understand how species diversity is formed and maintained. In this study, we used species inventories, a molecular phylogeny, and trait data to detect patterns of phylogenetic and functional community structure in successional plant communities growing on the mounds of Himalayan marmots (Marmota himalayana) on the southeast edge of the Qinghai-Tibet Plateau. We found that phylogenetic and functional diversities of plant communities on marmot mounds tended to cluster during the early to medium stages of succession, then trended toward overdispersion from medium to late stages. Alpine species in early and late stages of succession were phylogenetically and functionally overdispersed, suggesting that such communities were assembled mainly through species interactions, especially competition. At the medium and late stages of succession, alpine communities growing on marmot mounds were phylogenetically and functionally clustered, implying that the communities were primarily structured by environmental filtering. During the medium and late stages of succession the phylogenetic and functional structures of plant communities on marmot mounds differed significantly from those on neighboring sites. Our results indicate that environmental filtering and species interactions can change plant community composition at different successional stages. Assembly of plant communities on marmot mounds was promoted by a combination of traits that may provide advantages for survival and adaptation during periods of environmental change.

Differences between the child and adult brain in the local functional structure of the cerebral cortex

Imaging studies on neuronal network formation provide relevant information as to how the brain matures during adolescence. We used a novel imaging approach combining well-established MRI measures of local functional connectivity that jointly provide qualitatively different information relating to the functional structure of the cerebral cortex. To investigate the adolescent transition into adulthood, we comparatively assessed 169 preadolescents aged 8-12 years and 121 healthy adults. Whole-brain functional connectivity maps were generated using multi-distance measures of intracortical neural activity coupling defined within iso-distant local areas. Such Iso-Distant Average Correlation (IDAC) measures therefore represent the average temporal correlation of a given brain unit, or voxel, with other units situated at increasingly separated iso-distant intervals. The results indicated that between-group differences in the functional structure of the cerebral cortex are extensive and implicate part of the lateral prefrontal cortex, a medial frontal/anterior cingulate region, the superior parietal lobe extending to the somatosensory strip and posterior cingulate cortex, and local connections within the visual cortex, hippocampus, amygdala and insula. We thus provided detail of the cerebral cortex functional structure maturation during the transition to adulthood, which may serve to establish more accurate links between adolescent performance gains and cerebral cortex maturation. Remarkably, our study provides new information as to the cortical maturation processes in prefrontal areas relevant to executive functioning and rational learning, medial frontal areas playing an active role in the cognitive appraisal of emotion and anxiety, and superior parietal cortices strongly associated with bodily self-consciousness in the context of body image formation.

Detection of functional networks within white matter using independent component analysis

Spontaneous fluctuations in MRI signals from gray matter (GM) in the brain are interpreted as originating from variations in neural activity, and their inter-regional correlations may be analyzed to reveal functional connectivity. However, most studies of intrinsic neuronal activity have ignored the spontaneous fluctuations that also arise in white matter (WM). In this work, we explore spontaneous fluctuations in resting state MRI signals in WM based on spatial independent component analyses (ICA), a data-driven approach that separates signals into independent sources without making specific modeling assumptions. ICA has become widely accepted as a valuable approach for identifying functional connectivity within cortex but has been rarely applied to derive equivalent structures within WM. Here, BOLD signal changes in WM of a group of subjects performing motor tasks were first detected using ICA, and a spatial component whose time course was consistent with the task was found, demonstrating the analysis is sensitive to evoked BOLD signals in WM. Secondly, multiple spatial components were derived by applying ICA to identify those voxels in WM whose MRI signals showed similar temporal behaviors in a resting state. These functionally-related structures are grossly symmetric and coincide with corresponding tracts identified from diffusion MRI. Finally, functional connectivity was quantified by calculating correlations between pairs of structures to explore the synchronicity of resting state BOLD signals across WM regions, and the experimental results revealed that there exist two distinct groupings of functional correlations in WM tracts at rest. Our study provides further insights into the nature of activation patterns, functional responses and connectivity in WM, and support previous suggestions that BOLD signals in WM show similarities with cortical activations and are characterized by distinct underlying structures in tasks and at rest.

Degraded functional structure of macroinvertebrates caused by commercial sand dredging practices in a flood plain lake

In parts of developing countries, the over-exploitation of sands from inland waters has led to serious environmental concerns. However, understanding of the impacts of commercial sand dredging on inland water ecosystem functions remains limited. Herein, we assess the effects of this activity on the functional structure of the macroinvertebrate community and its recovery processes based on a 4-year survey, in the South Dongting Lake in China. Our result showed a simplified macroinvertebrate functional structures within the dredged area, as evidenced by a loss of certain trait categories (e.g., oval and conical body form) and a significant reduction in trait values due to the direct removal of macroinvertebrates and indirect alternations to physical environmental conditions (e.g., water depth and %Medium sand). Moreover, clear increases were observed in certain trait categories (e.g., small body size and swimmer) resulting from the dredging-related disturbance (e.g., increased turbidity) within the adjacent area. Furthermore, one year after the cessation of dredging, a marked recovery in the taxonomic and functional structure of macroinvertebrate assemblages was observed with most lost trait categories returning and an increase in the trait values of eight categories (e.g., body size 1.00-3.00 cm and oval body form) within the dredged and adjacent area. In addition, dispersal processes and sediment composition were the main driver for the structuring of the macroinvertebrate taxonomic and functional assemblages during the dredging stages, whilst water environmental conditions dominated the taxonomic structure and dispersal processes determined the functional structure during the recovery stage. Implications of our results for monitoring and management of this activity in inland waters are discussed.

Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil

While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.

Different responses of taxonomic and functional structures of stream macroinvertebrate communities to local stressors and regional factors in a subtropical biodiversity hotspot

Examining the relative contribution of local environmental stressors and regional factors in structuring biological communities is essential for biodiversity conservation and environmental assessment, yet their relative roles for different community characterizations remain elusive. Here, we examined the responses of taxonomic and functional structures of stream macroinvertebrate communities to local and regional factors across a human-induced environmental gradient in the Han River Basin, one subtropical biodiversity hotspot in China. Our objectives were: 1) to examine the responses of traditional taxonomic measures and functional traits to anthropogenic disturbances; 2) to compare the relative importance of environmental versus spatial variables and catchment-scale versus reach-scale variables for the two community characterizations. We found that both species and trait compositions performed well in differentiating anthropogenic disturbances, indicating that both taxonomic and functional structures of macroinvertebrate communities were strongly altered by human activities. Particularly, some traits related to life history (e.g., voltinism), resilience and resistance (e.g., adult flying ability) are well suited for predicting changes of communities towards anthropogenic disturbances owing to their mechanistic relationship with environmental gradients. We found that environmental variables played more important roles than spatial effects in structuring both taxonomic and functional facets of macroinvertebrate communities. Environmental filtering was more important in determining functional than taxonomic structure, and the opposite was true for spatial effects. In terms of environmental variables, catchment land-uses played the primary role in determining taxonomic composition, whereas reach-scale variables related to local habitat heterogeneity were more influential for functional structure. Our study highlights the importance of employing metacommunity perspectives and different community characterizations in both theoretical and applied research. For stream bioassessment and management, we argue that the combination of taxonomic and functional characterizations of community should be implemented, as different facets of biological communities responded to different types of anthropogenic disturbances.

Trait-based predation suitability offers insight into effects of changing prey communities

Increasing environmental pressures and human impacts are reshaping community structures and species interactions throughout all trophic levels. The morphological and behavioural characteristics of species communities contain key ecological information on why prey species appear attractive to predators but are rarely applied when exploring predator-prey (PP) relationships. Expanding our knowledge on how changing prey communities can alter the food resource suitability (RS) for predators is vital for understanding PP dynamics in changing ecosystems. Detailed predator diet data are commonly restricted to commercially important species and often not available over long temporal scales. To find out whether structural changes of prey communities impact the food RS for predator communities over space and time, we apply a novel framework to describe and interpret changes in predator diet-suitability based on predation-relevant traits of prey. We use information on described feeding links from the literature to compile the prey spectrum for each predator and subsequently translate the prey-species into a prey-trait spectrum. For each predator, we then calculate a frequency-based prey-trait affinity score and relate it to the available food resource pool, the community weighted means of prey traits, resulting in a prey-suitability measure. We aim to reveal whether a described multi-decadal change in the community structure of zoobenthos had an impact on the food suitability for the benthic-feeding fish in a coastal system of the Baltic Sea. We assess the direction of change in resource quality from the perspective of benthic-feeding fish and describe predator-specific responses to examine which species are likely to profit or be disadvantaged by changes in their prey spectrum. Furthermore, we test the relationship between functional diversity of prey communities and food suitability for predators, and whether predation linkage-structures are affected through prey community-changes. Our results show that changes in zoobenthic communities had a positive effect on the food suitability for most benthic-feeding fish, implying more suitable food resources. Species-specific responses of predators suggest varying plasticity to cope with prey assemblages of different trait compositions. Additionally, the functional diversity of zoobenthos had a positive effect on the food suitability for predator fish. The changing trait compositions of prey influenced the PP linkage-structure, indicating varying specialisation of benthic feeding fish towards available food resources. Our findings suggest that changing morphological characteristics of prey can impact food RS features for its predators. This approach enables long-term evaluation of prey quality characteristics where no detailed diet data is available and allows for cross-system comparison as it is not relying on taxonomic identities per se.