Lower Functional Diversity Research Articles

Thermophilic dark fermentation for hydrogen and volatile fatty acids production from breadcrumbs

Food waste poses significant environmental challenges, with Japan generating 100 million kg of bread waste annually. This study explores the potential of thermophilic dark fermentation to convert bread waste into hydrogen (H2) and volatile fatty acids (VFA). A 3-L continuous stirred-tank reactor (CSTR) was operated for 269 days using breadcrumb as feedstock. The highest H2 production rate of 7.0 L-H2 L−1 d−1 was achieved on day 52 with the production of acetate and butyrate. However, H2 production fluctuated significantly, correlated with the shifts of microbial community structure. Initially, Thermoanaerobacterium saccharolyticum, Thermocoprobibacter melissae, and Anaerocolumna jejuensis coexisted, but An. jejuensis outcompeted others during the deterioration phase, resulting in acetate accumulation without H2 production. Metabolic potential analysis using the phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) revealed that carbohydrate degradation was primarily carried out by An. jejuensis, while protein and lipid degradation involved diverse microbial members. The low functional diversity in carbohydrate degradation was a potential cause of instability. This study demonstrates the feasibility of using bread waste for H2 and VFA production, and provided insights into microbial dynamics essential for stable reactor performance.

Patterns and drivers in the functional diversity decomposition of invaded stream fish communities

AbstractAimThe assembly of real‐world ecological communities in human‐modified landscapes is influenced by a complex interplay of spatial, temporal, environmental and invasion gradients. However, understanding the relative importance of these drivers and their interactions in shaping functional assembly remains elusive. Our study aimed to investigate the relative influence of these drivers on the functional assembly of a stream fish metacommunity.LocationStreams of the Lake Balaton catchment, Hungary.MethodsWe analysed a long‐term (18‐year) dataset of the stream fish metacommunity, focusing on changes in functional diversity (Q), redundancy (R) and species dominance (D). Ternary diagrams were utilized to decompose functional diversity into Q, R and D components and to visualize diversity patterns. Linear mixed‐effect regression and separate structural equation models were employed to identify significant drivers of Q, R and D.ResultsNative fish communities exhibited low functional diversity (Q) but high redundancy (R) and dominance (D), indicating functional convergence and dominance. Stream habitat size, network position and associated spatial, physical and chemical gradients emerged as consistently significant drivers of D and R. Changes in Q were additionally linked to non‐native community properties and subtle shifts in land use and within‐stream habitat characteristics.Main ConclusionsOur findings suggest that both environmental filtering and interspecies interactions, particularly trait similarity between invaders and natives shape functional assembly of stream fish metacommunities. Despite minimal temporal directional changes, environmental drivers predominantly influence long‐term diversity patterns of native fish communities, overshadowing invasion effects. Our findings underscore the importance of considering both environmental filtering mechanisms and interspecies interactions in understanding functional assembly. Additionally, the joint application of diversity decomposition frameworks with predictive modelling provides comprehensive insight into patterns of functional diversity and assembly across ecological communities.

Community connectivity and local heterogeneity explain animal species co-occurrences within pond communities.

Metacommunity processes have the potential to determine most features of the community structure. However, species diversity has been the dominant focus of studies. Nestedness, modularity and checkerboard distribution of species occurrences are main components of biodiversity organisation. Within communities, these patterns emerge from the interaction between functional diversity, spatial heterogeneity and resource availability. Additionally, the connectivity determines the pool of species for community assembly and, eventually, the pattern of species co-occurrence within communities. Despite the recognised theoretical expectations, the change in occurrence patterns within communities along ecological gradients has seldom been considered. Here, we analyse the spatial occurrence of animal species along sampling units within 18 temporary ponds and its relationship with pond environments and geographic isolation. Isolated ponds presented a nested organisation of species with low spatial segregation-modularity and checkerboard-and the opposite was found for communities with high connectivity. A pattern putatively explained by high functional diversity in ponds with large connectivity and heterogeneity, which determines that species composition tracks changes in microhabitats. On the contrary, nestedness is promoted in dispersal-limited communities with low functional diversity, where microhabitat filters mainly affect richness without spatial replacement between functional groups. Vegetation biomass promotes nestedness, probably due to the observed increase in spatial variance in biomass with the mean biomass. Similarly, the richness of vegetation reduced the spatial segregation of animals within communities. This result may be due to the high plant diversity of the pond that is observed similarly along all sampling units, which promotes the spatial co-occurrence of species at this scale. In the study system, the spatial arrangement of species within communities is related to local drivers as heterogeneity and metacommunity processes by means of dispersal between communities. Patterns of species co-occurrence are interrelated with community biodiversity and species interactions, and consequently with most functional and structural properties of communities. These results indicate that understanding the interplay between metacommunity processes and co-occurrence patterns is probably more important than previously thought to understand biodiversity assembly and functioning.

Taxonomic and functional diversity of zooxanthellate corals and hydrocorals in Southwestern Atlantic reefs

The Southwestern Atlantic (SWA) harbors a relatively species poor but highly endemic coral assemblage due to historical processes, environmental and ecological drivers. Despite its low to moderate cover, corals still have a disproportionate contribution to ecosystem function and stability in this region. In the context of global change, it is imperative to know corals’ diversity and biogeographic patterns, yet a comprehensive approach is still missing for SWA corals. We integrated occurrence data from 21 sites and nine functional traits across 20 coral (scleractinian and hydrozoan) species to explore the taxonomic and functional diversity of coral assemblages in the SWA (1°N-27°S). We identified eight regions based on coral species composition, and then described their functional diversity using four metrics: functional richness (FRic), functional dispersion (FDis), functional evenness (FEve), and functional originality (FOri). Taxonomic and functional diversity peak between latitudes 13°S-20°S, decreasing with increasing distance from this diversity center, known as the Abrolhos Bank that harbors a wide continental platform. Our findings reveal a prevalent pattern of high functional redundancy across these eight regions (indicated by low functional originality), with species occupying the edges of the trait space (high functional evenness) and converging around few trait values (low functional dispersion). Such patterns resulted in low taxonomic and functional beta diversity and increased nestedness among regions caused by dispersal barriers and environmental filtering. The Southernmost region (24°-27°S) has the lowest taxonomic and functional diversity and comprises only two species that share similar traits, with these corals being: hermaphrodites, brooders and depth-tolerant, and having a wide corallite. As this region might become critical for corals in a future tropicalization scenario, tropical corals that share similar traits to those of the southernmost region can be more likely to thrive. Knowledge on taxonomic and functional diversity patterns can offer critical information to conservation by helping prioritizing areas with higher diversity and species with traits that enhance survival under climate change.

Decoupled response of microbial taxa and functions to nutrients: The role of stoichiometry in plantations

The resource quantity and elemental stoichiometry play pivotal roles in shaping belowground biodiversity. However, a significant knowledge gap remains regarding the influence of different plant communities established through monoculture plantations on soil fungi and bacteria's taxonomic and functional dynamics. This study aimed to elucidate the mechanisms underlying the regulation and adaptation of microbial communities at the taxonomic and functional levels in response to communities formed over 34 years through monoculture plantations of coniferous species (Japanese larch, Armand pine, and Chinese pine), deciduous forest species (Katsura), and natural shrubland species (Asian hazel and Liaotung oak) in the temperate climate. The taxonomic and functional classifications of fungi and bacteria were examined for the mineral topsoil (0–10 cm) using MiSeq-sequencing and annotation tools of microorganisms (FAPROTAX and Funguild). Soil bacterial (6.52 ± 0.15) and fungal (4.46 ± 0.12) OTUs' diversity and richness (5.83*103±100 and 1.12*103±46.4, respectively) were higher in the Katsura plantation compared to Armand pine and Chinese pine. This difference was attributed to low soil DOC/OP (24) and DON/OP (11) ratios in the Katsura, indicating that phosphorus availability increased microbial community diversity. The Chinese pine plantation exhibited low functional diversity (3.34 ± 0.04) and richness (45.2 ± 0.41) in bacterial and fungal communities (diversity 3.16 ± 0.15 and richness 56.8 ± 3.13), which could be attributed to the high C/N ratio (25) of litter. These findings suggested that ecological stoichiometry, such as of enzyme, litter C/N, soil DOC/DOP, and DON/DOP ratios, was a sign of the decoupling of soil microorganisms at the genetic and functional levels to land restoration by plantations. It was found that the stoichiometric ratios of plant biomass served as indicators of microbial functions, whereas the stoichiometric ratios of available nutrients in soil regulated microbial genetic diversity. Therefore, nutrient stoichiometry could serve as a strong predictor of microbial diversity and composition during forest restoration.

Dispersal constrains the biotic connectivity of mountain assemblages

AbstractAimClimate warming is shifting the bioclimatic optima of species towards mountaintops, but the ability of organisms to track these changes also depends on their dispersal skills. Here, we assessed the role of dispersal over niche‐driven processes in connecting assemblages along mountain slopes and between mountain massifs.LocationCantabrian Mountains, Spain.TaxonBirds (Animalia; Aves) and Lichens (Fungi; Ascomycota, Basidiomycota).MethodsWe examined the change with elevation of community‐level traits that are dispersal proxies (wing shape in birds and type of dispersing propagule in lichens) and ecological niche proxies (micro‐habitat, substrate, and foraging features). We then permutate species composition within sites and massifs to create models of species distribution constrained by dispersal and niche processes. These models were compared with observed species distribution to disclose the relative contribution of dispersal and niche‐based processes in the biotic interchange along mountain slopes (vertical connectivity) and between isolated summits (horizontal connectivity).ResultsBoth bird and lichen communities were formed by species with traits that enhance dispersal at high elevations. These groups also showed similarities in the elevational patterns of niche diversity, which dropped at high elevations. Dispersal was by far the dominant assembly mechanism in both taxa. Pairwise community comparisons among elevation belts showed weak vertical connectivity, with predominant dispersal limitations but also niche barriers between the extremes of the gradient. Among massifs, horizontal connectivity was higher among high mountain assemblages than those from lower elevations.Main ConclusionDispersal was found to be the dominant assembly mechanism in mountain systems, even in taxa with high dispersal potential. Highland assemblages had low functional diversity but their species had high mobility. This permits biotic interchange between isolated summits and, potentially, colonization of other summits as climate warms. Our framework combining traits and occurrence‐permutation models improve the understanding of community assembly mechanisms along elevation gradients and points to dispersal limitations, especially at low‐middle elevations.

Loss of functional diversity rather than species diversity of pollinators decreases community‐wide trait matching and pollination function

Abstract Loss of animal species and functional diversity can degrade ecosystem functions and services in plant–animal mutualistic networks, but their relative effects have rarely been previously examined in natural communities. Contrary to previously published theoretical results, under natural conditions, changes in pollinator functional niches caused by species and functional diversity losses are dynamic and often unpredictable. The lack of studies on natural networks limits our ability to predict future effects of decreasing pollinator diversity on wild and cultivated plants. We quantitatively evaluated the relative effects of pollinator species and functional diversity loss on plant–pollinator trait matching and pollination success across 40 spatiotemporally variable coastal networks. We found that low pollinator functional diversity (low abundance of long‐tongued pollinators) reduced community‐level plant functional specialization and trait matching between flowers and pollinators by reducing functional floral‐niche partitioning among pollinators. In contrast, pollinator species diversity did not influence community‐level trait matching. Furthermore, decreasing community‐level trait matching had a negative effect on community‐level plant pollination success, regardless of flower morphology. The present study demonstrated that pollinator functional diversity loss, rather than species diversity loss, was the main factor contributing to pollination functional loss in the plant–pollinator networks studied. We also demonstrated the importance of assessing functional aspects of plant–pollinator networks to evaluate community‐level pollination functional loss under global pollinator decline. Read the free Plain Language Summary for this article on the Journal blog.

Constraints on avian seed dispersal reduce potential for resilience in degraded tropical forests

Abstract Seed dispersal is fundamental to tropical forest resilience. Forest loss or degradation typically leads to defaunation, altering seed transfer dynamics and impairing the ability of forested habitats to regenerate or recover from perturbation. However, the extent of defaunation, and its likely impacts on the seed dispersers needed to restore highly degraded or clear‐felled areas, remains poorly understood in tropical forest landscapes. To quantify defaunation of seed‐dispersing birds, we used field survey data from 499 transects in three forested regions of Brazil, first comparing the observed assemblages with those predicted by geographic range maps, and then assessing habitat associations of frugivores across land cover gradients. We found that current bird assemblages have lower functional diversity (FD) than predicted by species range maps in Amazonia (4%–6%), with a greater reduction in FD (28%) for the Atlantic Forest, which has been more heavily deforested for a longer period. Direct measures of seed dispersal are difficult to obtain, so we focused on potential seed transfer inferred from shared species occurrence. Of 83 predominantly frugivorous bird species recorded in relatively intact forests, we show that 10% were absent from degraded forest, and 57% absent from the surrounding matrix of agricultural land covers, including many large‐gaped species. Of 112 frugivorous species using degraded forest, 47% were absent from matrix habitats. Overall, frugivores occurring in both intact forest and matrix habitats were outnumbered by (mostly small‐gaped) frugivores occurring in both degraded forest and matrix habitats (23 additional species; 64% higher diversity). These findings suggest that birds have the potential to disperse seeds from intact and degraded forest to adjacent cleared lands, but that direct seed transfer from intact forests is limited, particularly for large‐seeded trees. Degraded forests may play a vital role in supporting natural regeneration of small‐seeded tree species as well as providing a ‘stepping‐stone’ in the regeneration pathway for large‐seeded trees. We propose that both intact and degraded forests will support the restoration potential of tropical forest landscapes, and that bird‐assisted seed dispersal can be enhanced by maintaining buffer zones of degraded or secondary forests around remaining intact forest patches. Read the free Plain Language Summary for this article on the Journal blog.

Lichen-associated microbial members are prevalent in the snow microbiome of a sub-arctic alpine tundra.

Snow is the largest component of the cryosphere, with its cover and distribution rapidly decreasing over the last decade due to climate warming. It is imperative to characterize the snow (nival) microbial communities to better understand the role of microorganisms inhabiting these rapidly changing environments. Here, we investigated the core nival microbiome, the cultivable microbial members, and the microbial functional diversity of the remote Uapishka mountain range, a massif of alpine sub-arctic tundra and boreal forest. Snow samples were taken over a two-month interval along an altitude gradient with varying degree of anthropogenic traffic and vegetation cover. The core snow alpine tundra/boreal microbiome, which was present across all samples, constituted of Acetobacterales, Rhizobiales and Acidobacteriales bacterial orders, and of Mycosphaerellales and Lecanorales fungal orders, with the dominant fungal taxa being associated with lichens. The snow samples had low active functional diversity, with Richness values ranging from 0 to 19.5. The culture-based viable microbial enumeration ranged from 0 to 8.05×103 CFUs/mL. We isolated and whole-genome sequenced five microorganisms which included three fungi, one alga, and one potentially novel bacterium of the Lichenihabitans genus; all of which appear to be part of lichen-associated taxonomic clades.

Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils.

Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.

Green Roof Plant Traits: Influence of Functional Diversity on Ecosystem Services and Coexistence

Green roofs are a novel ecosystem incorporated into the urban landscape to increase green space and provide ecosystem services. Different plant traits excel at providing different green roof ecosystem services, leading to a growing demand for biodiverse green roofs. Research is needed to understand how plant biodiversity can be maintained over time on green roofs, and to determine which species combinations might maximize a given ecosystem service. In this three-year green roof experiment, we use 11 species incorporated into 7 species combinations to create treatments that vary in functional diversity, with treatments including species that are functionally similar, dissimilar, or of intermediate similarity. The selected species combinations were used to determine how trait diversity influences the key ecosystem services of stormwater retention, reduced substrate temperature, pollinator appeal (flower quantity), and the production of aboveground biomass. Additionally, we examine the likelihood of species survival and facilitation within each combination. Here, high functional diversity in leaf thickness and low functional diversity in height and leaf dry matter content was associated with increased biomass, while higher functional diversity in leaf thickness and root length density was associated with decreased substrate temperatures.

Effects of land cover and habitat condition on the bird community along a gradient of agricultural development within an arid watershed of Chile

Agricultural activities are a major cause of change in avifauna, frequently resulting in diminished diversity and biotic homogenization, and ultimately compromising ecosystem functioning and resilience. Arid ecosystems, which provide habitat for numerous native and endemic bird species, are vulnerable to global change and valuable in predicting future ecosystem shifts in regions undergoing aridification as a result of climate change. However, the impacts of agriculture on bird communities in arid ecosystems are understudied. Here, we evaluate these impacts in the arid Limarí watershed in north-central Chile, a region that has experienced extensive land use conversion to agriculture over the past 50 years. Specifically, we investigated current spatial patterns of avian beta diversity and the impact of landscape context on this diversity facet. Moreover, we evaluated how bird species respond to land cover and habitat conditions and the role of specific bird traits in this regard. To achieve this, we evaluated taxonomic and functional beta diversity across 26 sites distributed along a gradient of agricultural development, applied a beta diversity decomposition procedure, and carried out hierarchical joint species distribution modeling. Our study revealed high taxonomic but low functional beta diversity of the avifauna in the Limarí watershed, potentially indicative of past functional homogenization. Contrary to our initial expectations, present agricultural practices did not decrease beta diversity. While human-related landscape elements and agricultural features mostly had neutral or positive effects on bird occurrence, they negatively affected endemic species and certain bird traits related to diet and habitat. Riparian vegetation cover and quality, unrelated to agricultural and urban development, emerged as key factors structuring the regional bird community, and influenced beta diversity. Our results underscore the profound influence of land use change on the avian community in this arid region and the vital role of riparian ecosystems in this regard. Balancing conservation objectives with agricultural development is key to ensuring both the persistence of several functional groups in the region as well as the ecosystem services they provide.

Remotely sensed environmental data as ecological proxies for ground‐dwelling ant diversity along a subtropical forest succession gradient

Abstract Early naturalists such as Humboldt observed that changes in topography and anthropogenic disturbances influenced vegetation structure and the composition of animal communities. This holistic view of community assembly continues to shape conservation and restoration strategies in an era of landscape degradation and biodiversity loss. Today, remote sensing affords ecologists the tools for obtaining rapid and precise measures of topography, disturbance history and vegetation structure. Nonetheless, the capacity of such measures to predict the structure of diverse and functionally important insect communities has not been fully explored. We sampled ground‐dwelling ant assemblages with pitfall traps along a successional gradient (15 grasslands, 21 shrublands and 44 forests) in subtropical Asia, and measured the taxonomic (TD) and functional diversity (FD). We used airborne Light Detection and Ranging (LiDAR) and aerial photography—to measure topography, anthropogenic‐fire history and vegetation structure at each site. Using structural equation models, we tested the hypothesis that vegetation structure mediated the effects of topography and anthropogenic‐fire history on ant assemblage TD and FD, with stronger effects on the latter. We found that low elevation and anthropogenic‐fire history promoted ant TD, and by mediating vegetation structure, these factors further controlled ant FD. Specifically, assemblages of ant species occupying more similar niches—as indicated by their lower FD—were found in secondary forests that had more structurally homogeneous vegetation. These sites also had low insolation and high water moisture content, and were not recently burned as revealed by LiDAR‐derived metrics and aerial images. Furthermore, remotely sensed vegetation structures were closely associated with individual ant traits, such as body size and eye length, which reflect species' preferences for habitat structure. Synthesis. Our study uncovers the interactive effects of topography, disturbance history and vegetation structure in determining the TD and FD of ant assemblages in subtropical landscapes. Moreover, it demonstrates that remote sensed data can be leveraged to efficiently elucidate the complex effects of environmental change and disturbances on vegetation structure and consequently insect biodiversity, representing ecological proxies to refine ground investigation plans and support appropriate conservation and restoration measures for degraded landscapes.

Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis.

LncRNAs comprise a heterogeneous class of RNA-encoding genes typified by low expression, nuclear enrichment, high tissue-specificity, and functional diversity, but the vast majority remain uncharacterized. Here, we assembled the mouse liver noncoding transcriptome from >2000 bulk RNA-seq samples and discovered 48,261 liver-expressed lncRNAs, a majority novel. Using these lncRNAs as a single-cell transcriptomic reference set, we elucidated lncRNA dysregulation in mouse models of high fat diet-induced nonalcoholic steatohepatitis and carbon tetrachloride-induced liver fibrosis. Trajectory inference analysis revealed lncRNA zonation patterns across the liver lobule in each major liver cell population. Perturbations in lncRNA expression and zonation were common in several disease-associated liver cell types, including nonalcoholic steatohepatitis-associated macrophages, a hallmark of fatty liver disease progression, and collagen-producing myofibroblasts, a central feature of liver fibrosis. Single-cell-based gene regulatory network analysis using bigSCale2 linked individual lncRNAs to specific biological pathways, and network-essential regulatory lncRNAs with disease-associated functions were identified by their high network centrality metrics. For a subset of these lncRNAs, promoter sequences of the network-defined lncRNA target genes were significantly enriched for lncRNA triplex formation, providing independent mechanistic support for the lncRNA-target gene linkages predicted by the gene regulatory networks. These findings elucidate liver lncRNA cell-type specificities, spatial zonation patterns, associated regulatory networks, and temporal patterns of dysregulation during hepatic disease progression. A subset of the liver disease-associated regulatory lncRNAs identified have human orthologs and are promising candidates for biomarkers and therapeutic targets.

Heavy metal effects on multitrophic level microbial communities and insights for ecological restoration of an abandoned electroplating factory site

The response of soil microbes to heavy metal pollution provides a metric to evaluate the soil health and ecological risks associated with heavy metal contamination. However, a multitrophic level perspective of how soil microbial communities and their functions respond to long-term exposure of multiple heavy metals remains unclear. Herein, we examined variations in soil microbial (including protists and bacteria) diversity, functional guilds and interactions along a pronounced metal pollution gradient in a field surrounding an abandoned electroplating factory. Given the stressful soil environment resulting from extremely high heavy metal concentrations and low nutrients, beta diversity of protist increased, but that of bacteria decreased, at high versus low pollution sites. Additionally, the bacteria community showed low functional diversity and redundancy at the highly polluted sites. We further identified indicative genus and “generalists” in response to heavy metal pollution. Predatory protists in Cercozoa were the most sensitive protist taxa with respect to heavy metal pollution, whereas photosynthetic protists showed a tolerance for metal pollution and nutrient deficiency. The complexity of ecological networks increased, but the communication among the modules disappeared with increasing metal pollution levels. Subnetworks of tolerant bacteria displaying functional versatility (Blastococcus, Agromyces and Opitutus) and photosynthetic protists (microalgae) became more complex with increasing metal pollution levels, indicating their potential for use in bioremediation and restoration of abandoned industrial sites contaminated by heavy metals.

The Effect of Plant Diversity and Soil Properties on Soil Microbial Biomass and Activity in a Novel Ecosystem

Plant–microbial relations have not yet been fully disclosed in natural or seminatural ecosystems, nor in novel ecosystems developing spontaneously on post-coal mine heaps. The aim of this study was to determine which factor, biotic (plant taxonomic diversity vs. plant functional diversity) or abiotic (physicochemical substrate parameters), affects the biomass of soil microbial communities the most, as well as soil in situ respiration in novel ecosystems. The study was carried out on unreclaimed plots selected according to four different combinations of taxonomic and functional plant diversity. Additionally, plots on a reclaimed heap served as a comparison between the two management types. The biomass of several soil microbial groups was analysed using phospholipid fatty acids profiles. We detected that soil microbial biomass was more impacted by abiotic parameters (explaining 23% of variance) than plant diversity (explaining 12% of variance). Particularly, we observed that substrate pH was the most important factor shaping microbial community biomass, as shown in the RDA analysis. The highest microbial biomass was found in plots with low taxonomic and functional diversity. This finding can be explained by the fact that these plots represented a more advanced phase of vegetation development in the early stages of plant succession.

Multifaceted diversity changes reveal community assembly mechanisms during early stages of post-logging forest succession

Plant succession is a fundamental process of vegetation recovery on disturbed sites. Elucidating its mechanisms remains a challenge as succession is influenced by stochastic and deterministic processes related to abiotic and biotic filters. Here, we use a multifaceted diversity approach to reveal mechanisms of successional changes in European oak-hornbeam forests during the first 10 years after selective logging. As the mechanisms controlling succession may depend upon initial abiotic conditions and colonization potential of the surrounding vegetation, we compare changes in taxonomic, functional, and phylogenetic diversity between clearings connected with open habitats and those isolated inside forests. Despite fewer dispersal barriers and higher biomass production in connected clearings, similar mechanisms initially governed succession in post-logging sites. Both clearings had low taxonomic and functional diversity in the first year of succession, as evidenced by significant trait convergence, caused by the legacy of interactions between overstory and understory vegetation in pre-disturbance closed-canopy forests. Colonization by short-lived and light-demanding species in the second and third years after logging has markedly increased the overall taxonomic and functional diversity, as evidenced by significant trait divergence. Connected clearings had higher functional but lower taxonomic and phylogenetic diversity than isolated clearings from the fourth to ten years of succession, probably due to intense competition in more productive habitats. All diversity facets markedly decreased in the last years due to increasing asymmetric competition from regenerating trees. The successional processes were largely deterministic, driven by species’ life-history strategies and biotic interactions (competition) rather than abiotic constraints and stochastic events.

Diversity of benthic diatoms in the Baltic Sea: alpha and beta diversity, environmental drivers, and diversity-biomass relationships

Benthic diatoms are crucial for the functioning of ecosystems, but their diversity patterns along large gradients are poorly studied. By using 3 self-collected data sets along large environmental gradients in the Baltic Sea, represented over spatial scales of 60, 1300, and 2300 km, I investigated whether different aspects of diversity follow general patterns or are context- and region-specific. General diversity patterns along different gradients would likely indicate high resilience of benthic diatoms against differences and changes in the environment, whereas context-dependent patterns would possibly suggest that environmental change is likely to modify diatom communities and that region-specific differences should be considered when designing ecosystem management. I investigated the effect of environmental conditions on taxonomic and functional diatom diversity with distance-based redundancy analyses, variability of taxonomic diversity with species accumulation curves, taxonomic and functional aspects of spatial beta diversity with pairwise Bray-Curtis dissimilarity indices and Mantel tests, and diversity-biomass relationships with generalized linear models. The effect of environment on diatom communities was context-dependent, and different factors controlled communities along different gradients. Diversity varied along gradients and correlated with salinity in a U-shaped way. Beta diversity followed a general pattern of high taxonomic but low functional beta diversity along all gradients. Relationships between diatom diversity and ecosystem biomass were weak along all gradients. These results suggest that although the regional diversity of diatoms seems resilient, environmental change is likely to modify the local diversity of diatom communities. Finding out how these changes will affect ecosystem functioning requires further investigation.

Ocean acidification increases the impact of typhoons on algal communities

Long-term environmental change, sudden pulses of extreme perturbation, or a combination of both can trigger regime shifts by changing the processes and feedbacks which determine community assembly, structure, and function, altering the state of ecosystems. Our understanding of the mechanisms that stabilise against regime shifts or lock communities into altered states is limited, yet also critical to anticipating future states, preventing regime shifts, and reversing unwanted state change. Ocean acidification contributes to the restructuring and simplification of algal systems, however the mechanisms through which this occurs and whether additional drivers are involved requires further study. Using monthly surveys over three years at a shallow-water volcanic seep we examined how the composition of algal communities change seasonally and following periods of significant physical disturbance by typhoons at three levels of ocean acidification (equivalent to means of contemporary ∼350 and future ∼500 and 900 μatm pCO2). Sites exposed to acidification were increasingly monopolised by structurally simple, fast-growing turf algae, and were clearly different to structurally complex macrophyte-dominated reference sites. The distinct contemporary and acidified community states were stabilised and maintained at their respective sites by different mechanisms following seasonal typhoon disturbance. Macroalgal-dominated sites were resistant to typhoon damage. In contrast, significant losses of algal biomass represented a near total ecosystem reset by typhoons for the turf-dominated communities at the elevated pCO2 sites (i.e. negligible resistance). A combination of disturbance and subsequent turf recovery maintained the same simplified state between years (elevated CO2 levels promote turf growth following algal removal, inhibiting macroalgal recruitment). Thus, ocean acidification may promote shifts in algal systems towards degraded ecosystem states, and short-term disturbances which reset successional trajectories may ‘lock-in’ these alternative states of low structural and functional diversity.

Tissue-Specific Transcriptomes Outline Halophyte Adaptive Strategies in the Gray Mangrove (Avicennia marina)

Avicennia marina forests fulfill essential blue carbon and ecosystem services, including halting coastal erosion and supporting fisheries. Genetic studies of A. marina tissues could yield insight into halophyte adaptive strategies, empowering saline agriculture research. We compare transcriptomes from A. marina pneumatophores, stems, leaves, flowers, seeds, and transcriptomes across four widely divergent environments in the Indo-Pacific (Red Sea, Arabian Gulf, Bay of Bengal, and Red River Delta) to decipher the shared and location-, tissue-, and condition-specific functions. On average, 4.8% of transcripts per tissue were uniquely expressed in that tissue, and 12.2% were shared in all five tissues. Flowers’ transcript expression was the most distinct, with domain-centric gene ontology analysis showing high enrichment for stimulus-responsive processes, as well as genes implicated in flowering (hydroxygeraniol dehydrogenase, TPM = 3687) and floral scent biosynthesis (e.g., benzoyl_coenzyme_A, 2497.2 TPM). Pneumatophores highly expressed antioxidant genes, such as glutathione S-transferase (GST, TPM = 4759) and thioredoxin (TRX, TPM = 936.2), as well as proteins in the GO term ‘Hydroquinone:oxygen oxidoreductase activity’ (enrichment Z = 7.69, FDR-corr. p = 0.000785). Tissue-specific metabolic pathway reconstruction revealed unique processes in the five tissues; for example, seeds showed the most complete expression of lipid biosynthetic and degradation pathways. The leaf transcriptome had the lowest functional diversity among the expressed genes in any tissue, but highly expressed a catalase (TPM = 4181) and was enriched for the GO term ‘transmembrane transporter activity’ (GO:0015238; Z = 11.83; FDR-corr. p = 1.58 × 10−9), underscoring the genes for salt exporters. Metallothioneins (MTs) were the highest-expressed genes in all tissues from the cultivars of all locations; the dominant expression of these metal-binding and oxidative-stress control genes indicates they are essential for A. marina in its natural habitats. Our study yields insight into how A. marina tissue-specific gene expression supports halotolerance and other coastal adaptative strategies in this halophytic angiosperm.