Beta Diversity Patterns Research Articles

EDNA metabarcoding reveals the role of habitat specialization and spatial and environmental variability in shaping diversity patterns of fish metacommunities.

Information is scarce on how environmental and dispersal processes interact with biological features of the organisms, such as their habitat affinity, to influence patterns in biodiversity. We examined the role of habitat specialist vs. generalist species, and the spatial configuration, connectivity, and different environmental characteristics of river-floodplain habitats to get a more mechanistic understanding of alpha and beta diversity of fish metacommunities. We used environmental DNA metabarcoding to characterize species (taxa) richness and composition in two separate floodplains of the river Danube (Austria and Hungary) during two different hydrological conditions. Results showed that differences in the number of generalist and specialist species and their responses to connectivity and environmental gradients influenced patterns in alpha and beta diversity. Of the components of beta diversity, richness difference (nestedness) showed consistently higher values than replacement (turnover), mainly due to the decrease of specialist species along the connectivity gradient (i.e., from the mainstem to the most isolated oxbows). Variance in both alpha and beta diversity could be well predicted by a set of local and regional variables, despite high environmental variability, which characterizes river-floodplain ecosystems. Of these, the joint or shared variance fractions proved to be the most important, which indicates that the effects of local and regional processes cannot be unambiguously separated in these river-floodplain systems. Local scale environmental variables were more important determinants of both alpha and beta diversity in the low water period than in the high water period. These results indicate the differential role of local and regional processes in community organization during different hydrological conditions. Maintenance of both local and regional scale processes are thus important in the preservation of alpha and beta diversity of floodplain fish metacommunities, which should be considered by environmental management.

Patterns and drivers of avian taxonomic and phylogenetic beta diversity in China vary across geographical backgrounds and dispersal abilities.

Geographical background and dispersal ability may strongly influence assemblage dissimilarity; however, these aspects have generally been overlooked in previous large-scale beta diversity studies. Here, we examined whether the patterns and drivers of taxonomic beta diversity (TBD) and phylogenetic beta diversity (PBD) of breeding birds in China vary across (1) regions on both sides of the Hu Line, which demarcates China's topographical, climatic, economic, and social patterns, and (2) species with different dispersal ability. TBD and PBD were calculated and partitioned into turnover and nestedness components using a moving window approach. Variables representing climate, habitat heterogeneity, and habitat quality were employed to evaluate the effects of environmental filtering. Spatial distance was considered to assess the impact of dispersal limitation. Variance partitioning analysis was applied to assess the relative roles of these variables. In general, the values of TBD and PBD were high in mountainous areas and were largely determined by environmental filtering. However, different dominant environmental filters on either side of the Hu Line led to divergent beta diversity patterns. Specifically, climate-driven species turnover and habitat heterogeneity-related species nestedness dominated the regions east and west of the line, respectively. Additionally, bird species with stronger dispersal ability were more susceptible to environmental filtering, resulting in more homogeneous assemblages. Our results indicated that regions with distinctive geographical backgrounds may present different ecological factors that lead to divergent assemblage dissimilarity patterns, and dispersal ability determines the response of assemblages to these ecological factors. Identifying a single universal explanation for the observed pattern without considering these aspects may lead to simplistic or incomplete conclusions. Consequently, a comprehensive understanding of large-scale beta diversity patterns and effective planning of conservation strategies necessitate the consideration of both geographical background and species dispersal ability.

Deterministic processes drive turnover-dominated beta diversity of breeding birds along the central Himalayan elevation gradient

Beta diversity, the variation of community composition among sites, bridges alpha and gamma diversity and can reveal the mechanisms of community assembly through applying distance-decay models and/or partitioning beta diversity into turnover and nestedness components from functional and phylogenetic perspectives. Mountains as the most natural experiment system provide good opportunities for exploring beta diversity patterns and the underlying ecological processes. Here, we simultaneously consider distance-decay models and multiple dimensions of beta diversity to examine spatial variations of bird communities, and to evaluate the relative importance of niche-based and neutral community assembly mechanisms along a 3600-m elevational gradient in the central Himalayas, China. Our results showed that species turnover dominates taxonomic, functional, and phylogenetic beta diversity. We observed strongest evidence of spatial distance decays in taxonomic similarities of birds, followed by its phylogenetic and functional analogues. Turnover component was highest in taxonomic beta diversity, while nestedness component was highest in functional beta diversity. Further, all correlations of assemblage similarity with climatic distance were higher than that with spatial distances. Standardized values of overall taxonomic, functional, and phylogenetic beta diversity and their turnover components increase with increasing elevational distance, while the standardized values of taxonomic and phylogenetic nestedness decreased with increasing elevational distance. Our results highlighted the niche-based deterministic processes in shaping elevational bird diversity patterns that were determined by the relative roles of decreasing trend of environmental filtering and increasing trend of limiting similarity along elevation distances.

Spatial patterns of beta diversity in marine benthic assemblages from coastal areas of southern Brazil and their implications for conservation

Beta diversity helps to understand changes in species composition over space and time, with two key components: nestedness (hierarchical pattern in richer sites) and turnover (species replacement due to niche or dispersal differences). It measures the loss or gain of species (nestedness) and species replacement (turnover) when comparing two or more spatial/temporal/environmental units. As both components require different species conservation strategies, assessing which of them the communities are organized is an important tool for this purpose. Our study aimed to evaluate which two components of beta diversity (nestedness or turnover) are responsible for structuring invertebrate and fish assemblages on the southern coast of Brazil. This region is historically recognized as a shrimp trawling area, a type of fishing with negative impacts on marine biota, such as the removal of species and habitat destruction. Our results suggest that the overall beta diversity values demonstrated a high environmental heterogeneity among the sampled areas. The most significant fraction of the general beta diversity for both assemblages is explained by the spatial turnover component. As depth increased, there was a significant rise in overall beta diversity and species turnover for fish and invertebrate assemblages. In contrast, there were no significant correlations among the nestedness component, the geographical distance and depth. In water mass conditions, fish assemblage decreased with rising chlorophyll and decreasing temperature. Elevated marine phosphate and thick sediments adversely impacted invertebrate composition. Additionally, invertebrate richness showed a positive correlation with fine sand grains. The research conducted along the southern coast of Brazil suggests the utmost importance of these regions in terms of species conservation. Here, the dominant influence of the turnover component shapes the organization of subtropical marine benthic assemblages. Furthermore, these areas receive frequent visits from migratory species, further accentuating their ecological significance.

Regional climate contributes more than geographic distance to beta diversity of copepods (Crustacea Copepoda) between caves of Italy

Despite the study of subterranean biodiversity facing harsh sampling and mapping challenges, the huge diversity of taxa, ecological adaptations and evolutionary trajectories in subterranean environments is gaining increasing attention. Yet, the spatial and environmental factors driving the composition of groundwater communities are still poorly understood. To partially fill this knowledge gap, we collected copepod crustaceans from 12 caves along the Italian peninsula between 2019 and 2022, sampling each cave twice. The resulting presence-absence data were analysed to assess: (i) between-cave taxonomic beta diversity, also partitioning between turnover and nestedness-resultant dissimilarity; (ii) the relative weight of geographic distance and climatic differences in shaping observed beta diversity. Seventy-one species of copepods were collected overall. Pairwise beta diversity was high for most pairs of caves, with turnover being the major component. Geographic distance-decay models partially explained total beta diversity and turnover patterns. However, in Generalized Dissimilarity Models (GDM), including surface climatic conditions as predictors, the contribution of seasonal temperature averages was generally higher than that of geographic distance. Further, the explanatory and predictive performance of the GDMs notably increased, along with temperature contribution, when widening the spatial extent from which climate data were gathered. Our results confirmed a high spatial turnover in groundwater copepods’ assemblages and strengthened the link between regional climate and subterranean biodiversity.

Local and regional diversity of frog communities along an extensive rainforest elevation gradient in Papua New Guinea

AbstractRainforests on high tropical mountains are globally important species diversity hotspots. We studied amphibians along an extensive rainforest elevation gradient on Mt. Wilhelm (4509 m) in Papua New Guinea. We established eight sites at 500 m elevation increments between 200 and 3700 m a.s.l. and relate their community composition to the known species pool of New Guinea island. We recorded 3390 frogs from 55 species, which is three times more species than at any local community along the elevation gradient. Species diversity peaked at 1700 m a.s.l. for Mt. Wilhelm communities, and at 500–1100 m a.s.l. in the broader New Guinea fauna, probably reflecting increasing speciation and decreasing dispersal rates with increasing elevation. The beta diversity between frog communities was high and increased with increasing elevation. The change in frog community composition across 500 m elevation corresponded to the change over 200 km distance within lowland forests. A majority of frog species were distributed over narrow <500 m elevational ranges, at Mt Wilhelm and the New Guinea fauna more broadly. We did not detect Rapoport's pattern of wider elevation range for species at higher elevations than for lowland species, for Mt. Wilhelm communities or the New Guinea fauna. The high beta diversity patterns along elevation gradients generated by rapid species turnover with narrow elevation ranges make frog communities vulnerable to change in environment, including climate change.Abstract in Melanesian Pidgin is available with online material.

Interactions between soil bacterial communities, assembly processes and microbial functions along the elevational gradient

The distribution of microbial communities along elevational gradients has been widely reported, but whether there are linkages between soil microbial diversity, community assembly processes and microbial functions in elevational patterns, and whether the patterns are influenced by micro-topography (e.g. slope direction), remain unclear. Here, we collected soils from two slope directions (i.e. north-facing slope and east-facing slope) along the elevational gradient (∼2000 m elevational range) of a mountain ecosystem. Unexpectedly, for bacterial alpha diversity or microbial functions (i.e. multifunctionality), we found consistent elevational patterns for both slope directions, with alpha diversity showing a hump-shaped pattern and microbial functions exhibiting a linearly increasing trend. Similarly, for both slope directions, there were significant elevational distance-decay relationships in the bacterial beta diversity pattern. The elevational patterns of soil bacterial diversity were determined by the transitions of community assembly processes, while microbial functions were mainly influenced by bacterial community composition. These results suggest that soil bacterial diversity, community assembly processes and microbial functions are interactive along an elevational gradient, and that these interactions are independent of slope direction. Our study adds new insights into the elevational patterns of soil bacterial communities and their drivers and ecological consequences in mountain ecosystems.

Macroinvertebrates beta diversity and responses of functional traits to water environmental factors in the Qingyijiang River, China

AbstractThe diversity of functional traits of macroinvertebrates in freshwater ecosystems is one of the current research hotspots in the field of biodiversity. Understanding the functional trait composition of macroinvertebrates and their factors can make the study of watershed beta diversity and river ecological security patterns more effective. Based on two field surveys conducted in September 2020 and July 2021 in the Qingyijiang (QYJ) River, the longest tributary on the south bank of the lower Yangtze River in China, we explored the functional trait compositions of macroinvertebrates and relationships between functional traits and water environment factors using functional diversity indices, beta diversity decomposition, R‐mode linked to Q‐mode, and fourth‐corner analysis methods. Our results showed that water environmental factors affected the distribution of macroinvertebrates traits, and the degree of effect was reflected by the correlation between water environmental factors and the abundance of species traits. Physical factors like flow velocity and water depth were significantly correlated with biological traits of species such as body size and swimming ability. In counterparts, some nutrient indicators significantly affected species ecological traits, such as total phosphorus, ammonia nitrogen, and chemical oxygen demand, which affected species habits and functional feeding group traits. At the same time, we also found a high turnover rate between communities in the river, reflecting the strong dispersal ability of the species. This will be an important guide for the conservation of macroinvertebrates diversity in the river. Local governments can take measures such as conducting quarterly monitoring of macroinvertebrates species; restoring riparian vegetation; limiting hardening of riverbanks and dredging of rivers; controlling wastewater discharges from residential areas on both sides of the river; controlling the use of pesticides in agricultural lands, and so on. These will become the key directions for the conservation of macroinvertebrates diversity.

Mock community experiments can inform on the reliability of eDNA metabarcoding data: a case study on marine phytoplankton

Environmental DNA metabarcoding is increasingly implemented in biodiversity monitoring, including phytoplankton studies. Using 21 mock communities composed of seven unicellular diatom and dinoflagellate algae, assembled with different composition and abundance by controlling the number of cells, we tested the accuracy of an eDNA metabarcoding protocol in reconstructing patterns of alpha and beta diversity. This approach allowed us to directly evaluate both qualitative and quantitative metabarcoding estimates. Our results showed non-negligible rates (17–25%) of false negatives (i.e., failure to detect a taxon in a community where it was included), for three taxa. This led to a statistically significant underestimation of metabarcoding-derived alpha diversity (Wilcoxon p = 0.02), with the detected species richness being lower than expected (based on cell numbers) in 8/21 mock communities. Considering beta diversity, the correlation between metabarcoding-derived and expected community dissimilarities was significant but not strong (R2 = 0.41), indicating suboptimal accuracy of metabarcoding results. Average biovolume and rDNA gene copy number were estimated for the seven taxa, highlighting a potential, though not exhaustive, role of the latter in explaining the recorded biases. Our findings highlight the importance of mock communities for assessing the reliability of phytoplankton eDNA metabarcoding studies and identifying their limitations.

Differential patterns of taxonomic and functional diversity for two groups of canopy arthropods across spatial scales

AbstractArthropod diversity is often linked to variation in resource use, dispersal ability, habitat connectivity, and climate factors that differ across spatial scales. The aim of this research was to examine how species richness, functional diversity, and community composition of two taxa differing in functional roles and dispersal ability are structured across spatial scales and to identify the importance of vegetation, climate, and landscape in explaining these patterns at different scales. Organisms were collected from tree canopies using insecticidal fogging in the summer of 2000 from 96 trees in 24 stands of 6 deciduous forest sites in 2 ecoregions of the eastern United States. Taxonomic and functional beta diversity of ants (Hymenoptera: Formicidae) and spiders (Araneae) were partitioned across four hierarchical spatial scales (individual tree, forest stand, site, and ecoregion). The contributions of climatic, landscape, and vegetation variables were determined using model selection. Ant and spider species richness, functional diversity, and community composition differed between taxa and across spatial scales. Alpha diversity (within trees) was lower than expected for both taxa and types of diversity, with host tree species supporting different species of ants and spiders. While the beta components of species diversity among trees and forest stands were greater than expected for both taxa, spiders also showed significant levels of beta diversity among sites. Functional beta diversity was less scale‐dependent than taxonomic beta diversity. Stand‐level patterns of beta diversity were significantly predicted by variation in climate and landscape connectivity. The effects of climate and landscape fragmentation on the diversity and community structure of both taxa indicate that anthropogenic climate change and land use change will alter canopy arthropod communities. Results also suggest that patterns of diversity among fragmentation metrics are influenced by differences in dispersal ability.

Dynamic patterns of beta diversity in the Anthropocene: incorporating moderators into dissimilarity-based models

Dynamic patterns of beta diversity in the Anthropocene: incorporating moderators into dissimilarity-based models

Life forms affect beta-diversity patterns of larch forests in China

Beta-diversity reflects the spatial changes in community species composition which helps to understand how communities are assembled and biodiversity is formed and maintained. Larch (Larix) forests, which are coniferous forests widely distributed in the mountainous and plateau areas in North and Southwest China, are critical for maintaining the environmental conditions and species diversity. Few studies of larch forests have examined the beta-diversity and its constituent components (species turnover and nestedness-resultant components). Here, we used 483 larch forest plots to determine the total beta-diversity and its components in different life forms (i.e., tree, shrub, and herb) of larch forests in China and to evaluate the main drivers that underlie this beta-diversity. We found that total beta-diversity of larch forests was mainly dependent on the species turnover component. In all life forms, total beta-diversity and the species turnover component increased with increasing geographic, elevational, current climatic, and paleoclimatic distances. In contrast, the nestedness-resultant component decreased across these same distances. Geographic and environmental factors explained 20%–25% of total beta-diversity, 18%–27% of species turnover component, and 4%–16% of nestedness-resultant component. Larch forest types significantly affected total beta-diversity and species turnover component. Taken together, our results indicate that life forms affect beta-diversity patterns of larch forests in China, and that beta-diversity is driven by both niche differentiation and dispersal limitation. Our findings help to greatly understand the mechanisms of community assemblies of larch forests in China.

Explaining the anuran beta diversity by pond‐living tadpoles: the role of dispersal limitation and environmental gradients through multiple scales

AbstractAimDetermining drivers of beta diversity is a hugely complex task, as it involves processes acting synergistically across multiple scales. We employed a large‐scale standardized protocol to tease apart the environmental and spatial processes driving beta diversity patterns of pond‐living tadpoles across multiple scales.LocationPonds distributed across 5000,000 km2 in five Brazilian biomes (Amazon, Atlantic Forest, Caatinga, Cerrado and Pantanal).MethodsWe sampled tadpoles in three to eight locations in each biome and eight to 61 ponds per location. We used partial distance‐based redundancy analyses with variation partitioning to assess the relative influence of environmental and spatial variables on beta diversity, which was estimated using the Raup–Crick index. We applied the same statistical protocol to the analyses conducted at the three spatial scales (metacommunity, regional and subcontinental), consistently maintaining the same grain while increasing the geographic extent.ResultsSpatially structured environmental variation was the most important driver of anuran beta diversity. At the regional scale, the spatial component was as important as spatially structured environmental variation, and the environmental component was the most important at the metacommunity scale. Narrow‐ranged and widespread species responded equally to environmental variables, but spatially structured environmental variation was more important to widespread species and pure spatial component was more important to narrow‐ranged species.Main ConclusionsOur results demonstrate that spatial scale plays a role in understanding the dispersal‐ and niche‐based processes that generate beta diversity patterns. Increasing the geographical extent increases the impact of spatial processes and the influence of environmental factors on anuran beta diversity through spatially structured environmental variation. Even under different environmental conditions, narrow‐ranged and widespread species respond in a consistent manner to environmental and spatial dynamics, showing consistent responses to niche‐ and dispersal processes. This evidence can offer important guidelines for their conservation even for large‐scale management that includes multiple biomes.

Multidimensional beta-diversity across local and regional scales in a Chinese subtropical forest: The role of forest structure.

Beta-diversity, or the spatio-temporal variation in community composition, can be partitioned into turnover and nestedness components in a multidimensional framework. Forest structure, including comprehensive characteristics of vertical and horizontal complexity, strongly affects species composition and its spatial variation. However, the effects of forest structure on beta-diversity patterns in multidimensional and multiple-scale contexts are poorly understood. Here, we assessed beta-diversity at local (a 20-ha forest dynamics plot) and regional (a plot network composed of 19 1-ha plots) scales in a Chinese subtropical evergreen broad-leaved forest. We then evaluated the relative importance of forest structure, topography, and spatial structure on beta-diversity and its turnover and nestedness components in taxonomic, functional, and phylogenetic dimensions at local and regional scales. We derived forest structural parameters from both unmanned aerial vehicle light detection and ranging (UAV LiDAR) data and plot inventory data. Turnover component dominated total beta-diversity for all dimensions at the two scales. With the exception of some components (taxonomic and functional turnover at the local scale; functional nestedness at the regional scale), environmental factors (i.e., topography and forest structure) contributed more than pure spatial variation. Explanations of forest structure for beta-diversity and its component patterns at the local scale were higher than those at the regional scale. The joint effects of spatial structure and forest structure influenced component patterns in all dimensions (except for functional turnover) to some extent at the local scale, while pure forest structure influenced taxonomic and phylogenetic nestedness patterns to some extent at the regional scale. Our results highlight the importance and scale dependence of forest structure in shaping multidimensional beta-diversity and its component patterns. Clearly, further studies need to link forest structure directly to ecological processes (e.g., asymmetric light competition and disturbance dynamics) and explore its roles in biodiversity maintenance.

Inferring alpha, beta, and gamma plant diversity across biomes with GEDI spaceborne lidar

Biodiversity-structure relationships (BSRs), which describe the correlation between biodiversity and three-dimensional forest structure, have been used to map spatial patterns in biodiversity based on forest structural attributes derived from lidar. However, with the advent of spaceborne lidar like the Global Ecosystem Dynamics Investigation (GEDI), investigators are confronted with how to predict biodiversity from discrete GEDI footprints, sampled discontinuously across the Earth surface and often spatially offset from where diversity was measured in the field. In this study, we used National Ecological Observation Network data in a hierarchical modeling framework to assess how spatially-coincident BSRs (where field-observed taxonomic diversity measurements and structural data from airborne lidar coincide at a single plot) compare with BSRs based on statistical aggregates of proximate, but spatially-dispersed GEDI samples of structure. Despite substantial ecoregional variation, results confirm cross-biome consistency in the relationship between plant/tree alpha diversity and spatially-coincident lidar data, including structural data from outside the field plot where diversity was measured. Moreover, we found that generalized forest structural profiles derived from GEDI footprint aggregates were consistently related to tree alpha diversity, as well as cross-biome patterns in beta and gamma diversity. These findings suggest that characteristic forest structural profiles generated from aggregated GEDI footprints are effective for BSR diversity prediction without incorporation of more standard predictors of biodiversity like climate, topography, or optical reflectance. Cross-scale comparisons between airborne- and GEDI-derived structural profiles provide guidance for balancing scale-dependent trade-offs between spatial proximity and sample size for BSR-based prediction with GEDI gridded products. This study fills a critical gap in our understanding of how generalized forest structural attributes can be used to infer specific field-observed biodiversity patterns, including those not directly observable from remote sensing instruments. Moreover, it bolsters the empirical basis for global-scale biodiversity prediction with GEDI spaceborne lidar.

Environmental Filtering and Dispersal Limitations Driving the Beta Diversity Patterns at Different Scales of Secondary Evergreen Broadleaved Forests in the Suburbs of Hangzhou.

Subtropical suburban secondary evergreen broadleaved forests are essential in regulating the ecological environment's quality and promoting urban sustainable development. In the suburbs of Hangzhou City, well-preserved secondary evergreen broadleaved forest communities were selected to establish a 6 ha forest dynamic monitoring plot. Community surveys and environmental factor measurements were conducted in this area. This study investigated the beta diversity patterns at different scales by considering the environmental and spatial factors to explore the driving beta diversity. Using a similar paired-site beta diversity decomposition method, the study aimed to investigate the differences in species composition and the mechanisms of multiple species coexistence within the secondary evergreen broadleaved forest communities. The results showed that the beta diversity of the suburban secondary evergreen broadleaved forest communities decreased with the increasing spatial scale. Both the dispersal limitation and the environmental filtering were found to drive the formation of beta diversity patterns in these subtropical suburban forests. At relatively smaller scales (<100 m), species turnover was found to determine the beta diversity patterns of the suburban secondary evergreen broadleaved forests. Dispersal limitation had a dominant influence at more minor scales, while the effect of environmental filtering gradually increased with scale, and the impact of the dispersal limitation decreased. The partitioning of the beta diversity in subtropical secondary evergreen broadleaved forests in China provides critical scientific insights into the spatial distribution patterns and changes in biodiversity. It offers valuable knowledge for the conservation and understanding of biodiversity maintenance in the region.

Reduced enumeration effort, but not coarse taxonomic resolution, is sufficient to represent beta diversity patterns of stream benthic diatoms

The use of reduced enumeration effort and coarse taxonomic resolutions are potential strategies for cost-effective biomonitoring programs and biological assessments. We evaluated whether reduced enumeration efforts (i.e., subsets of counted valves per sample) and identification to the genus level are sufficient to recover beta diversity patterns of benthic diatom metacommunities. Diatoms were sampled in 90 riffles within nine near-pristine subtropical streams. We found that reduced enumeration efforts were suitable to depict patterns both in the compositions of the communities and in biotic heterogeneity among streams produced by the original dataset (i.e., species-level identifications and 500 valves counted per riffle, the local community). A total of 400 and 50 valves were necessary to obtain similar compositional patterns observed using full samples identified at the species level for presence-absence and abundance data, respectively. Furthermore, biotic heterogeneity patterns among streams were recovered with 200 valves per local community for both presence-absence and abundance data. Identification to the genus level only reflected species-level compositional patterns when abundance data were used. However, the use of genus was not effective in depicting biotic heterogeneity patterns, independent of the enumeration effort. These results indicate that it is possible to reduce enumeration efforts, but not taxonomic resolution, to detect subtle regional biodiversity patterns of benthic diatoms in subtropical streams not subjected to strong environmental gradients. This is especially important due to the financial challenges faced by ecological and applied monitoring programs in tropical regions.

Revisiting Alwyn H. Gentry’s forest transect data: latitudinal beta diversity patterns are revealed using a statistical sampling-model-based approach

Gentry’s forest transect data have been frequently used to assess global patterns of plant diversity and plant species compositional changes along environmental and geographical gradients. Based on the worldwide woody plant abundance records from Gentry’s 197 localities/plots (each consisting of ten 2 m × 50 m subplots/transects), we apply a recently developed sampling-model-based standardization method (iNEXT.beta3D standardization) to examine how beta diversity among subplots varies with latitude. Beta diversity quantifies the extent of among-subplot differentiation which represents the interacting effect of species abundance distribution and spatial aggregation. Here beta diversity is obtained by a multiplicative decomposition scheme based on the framework of Hill numbers of any order q ≥ 0. Under statistical sampling models, data in nearly all of the 197 localities were incomplete, i.e., there were species present in the assemblage but undetected in the data. For Gentry’s data collected along narrow transects, the dependence among sampled individuals due to spatial aggregation is generally weak. The observed beta diversity depends on the among-subplot differentiation and sampling effort/completeness, which in turn induce dependence of the observed beta diversity on alpha and gamma diversity. To control for sampling effort/completeness, the iNEXT.beta3D method standardizes both alpha and gamma diversity at the same level of sample coverage to formulate coverage-based beta diversity. The resulting standardized beta diversity provides a statistical solution to remove the dependence of beta diversity on both alpha and gamma diversities, and thus reflects the pure among-subplot differentiation. The coverage-based standardization reveals latitudinal beta diversity patterns/trends not only for richness-based, but also for abundance-sensitive beta diversity.

Sources of gut microbiota variation in a large longitudinal Finnish infant cohort.

Although the infant gut microbiota has been extensively studied, comprehensive assessment on the microbiota determinants including technical variables has not been performed in large infant cohorts. We studied the effect of 109 variables on the 16S rRNA gene amplicon-based gut microbiota profiles of infants sampled longitudinally from three weeks to two years of life in the Finnish HELMi birth cohort. Spot faecal samples from both parents were included for intra-family analyses, totalling to 7657 samples from 985 families that were evaluated for beta-diversity patterns using permutational multivariate analysis on Bray-Curtis distances, and differential abundance testing and alpha-diversity for variables of interest. We also assessed the effect of different taxonomic levels and distance methods. In time point-specific models, the largest share of variation explained, up to 2-6%, were seen in decreasing order for the DNA extraction batch, delivery mode and related perinatal exposures, defecation frequency and parity/siblings. Variables describing the infant gastrointestinal function were continuously important during the first two years, reflecting changes in e.g., feeding habits. The effect of parity/siblings on infant microbiota was modified by birth mode and exposure to intrapartum antibiotics, exemplifying the tight interlinkage of perinatal factors relevant for infant microbiota research. In total, up to 19% of the biological microbiota variation in the infant gut could be explained. Our results highlight the need to interpret variance partitioning results in the context of each cohort's characteristics and microbiota processing. Our study provides a comprehensive report of key factors associated with infant gut microbiota composition across the two first years of life in a homogenous cohort. The study highlights possible important future research areas and confounding factors to be considered. This research was supported by Business Finland, Academy of Finland, Foundation for Nutrition Research and the Doctoral Program in Microbiology and Biotechnology, University of Helsinki, Finland.

Conserved Covarying Gut Microbial Network in Preterm Infants and Childhood Growth During the First 5 Years of Life: A Prospective Cohort Study

BackgroundLongitudinally conserved microbe-microbe interactions may provide insights to understand the complex dynamic system of early-life gut microbiota among preterm infants. ObjectivesWe aimed to profile the covarying network of gut microbiota among preterm infants and investigate its potential influence on host growth (2–5 y). MethodsWe collected time-series stool samples (n = 717 from children and n = 116 from mothers) among 51 preterm and 51 full-term infants from birth up to 5 y of age and among 53 mothers. The included infants underwent time-series measurements of early-life gut microbiota (0–5 y) and growth (2–5 y) from June 2014 to April 2017. The covarying taxa that exhibited consistent covariation from day 1 to year 5 were defined as conserved features in the development of gut microbiota. Childrens’ height-for-age z score (HAZ) and weight-for-age z score were calculated according to World Health Organization Child Growth Standards. ResultsWe observed distinct dynamic patterns of both microbial alpha and beta diversity comparing preterm infants with full-term controls during the very early stage (<3 mo). Moreover, we identified a covarying network containing 10 taxa as a conserved gut microbial feature of these preterm infants from birth to 5 y old. This covarying network was distinctive between preterm and full-term infants before 3 mo of age (P < 0.001) and tended to be similar as the infants grew up. Several covarying taxa of the network during early life (<3 mo) were associated with childhood growth (2–5 y) (eg, Clostridium_sensu_stricto_1 with HAZ, β = -0.32, q < 0.01), and the human milk feeding duration was a main modulating factor. ConclusionsPreterm born children possess conserved and distinct covarying microbiota during very early life, which may have a profound influence on their growth later in life.This trial was registered at clinicaltrials.gov as NCT03373721.