Distinct Biogeographic Regions Research Articles

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

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

Fishes of the upper rio Paraná basin: diversity, biogeography and conservation

Abstract The upper rio Paraná basin drains the most developed and environmentally degraded region in South America: the Brazilian southeast. While it is one of the most well-known Neotropical fish assemblages, it is also one of the most threatened by anthropic activity. Urbanization, deforestation, dam construction, invasive species, and water pollution not only reduce the living area of species but also alter our perception of the basin and its biotic elements. Such changes are so profound and pervasive that raise uncertainties about the native or non-native status of several species. This paper aims to offer a detailed picture of the native diversity and historical biogeography of the fishes in the upper rio Paraná basin, which we hope will offer a solid foundation for future conservation policies. We update the list of native species, analyze geographical distributions, and identify biogeographical patterns, emphasizing areas requiring recognition as distinct biotas for conservation efforts. Over the past 15 years, more than 100 additional species have been described or recorded, expanding the total to 341 native species belonging to six orders and 30 families, making it the richest river basin in Brazil outside the Amazonian region. Unlike most neotropical basins where Characidae dominates, loricariids make up nearly one-fourth of the total fish diversity in the region. Species and clades concentrate in the central basin, while endemics are confined to peripheral areas due to the complex biogeographical history shared with neighboring basins. Eighteen distinct biogeographical regions are identified, discussing their composition, histories, and conservation implications. The upper rio Paraná basin has 10% of its fish fauna ranked as endangered and present 128 non-native species, including three hybrids. This places it as the major drainage with the largest number of endangered taxa in the neotropics and at the same time the one with the most numerous non-native elements. Existing protected areas are deemed ineffective in preserving diverse assemblages and fail to safeguard the majority of threatened and narrowly-endemic species.

Atlantification influences zooplankton communities seasonally in the northern Barents Sea and Arctic Ocean

The Barents Sea is undergoing rapid ocean warming with less sea ice and increased Atlantic inflow, shifting the pelagic ecosystem towards a more boreal one, a process referred to as Atlantification. While such changes have already been documented in the southern and central Barents Sea, less is known about the degree of Atlantification in the northern Barents Sea and Arctic Ocean. In this seasonal study, we identified the mesozooplankton biodiversity, abundance and biomass in the Northern Barents Sea along a transect with seven stations stretching from the central Barents Sea (76°N) across the shelf break and into the Arctic Ocean (82°N) in August and December 2019, and March, May and July 2021. The broad range of mesozooplankton taxa and sizes were collected by conducting duplicate depth-stratified tows using alternate nets of mesh-sizes 64 µm and 180 µm. The majority of zooplankton taxa were ubiquitous in the study area, but the abundances and life stages varied depending on the season, region and the dominant water mass. We identified three distinct biogeographical regions with different zooplankton diversity and seasonal dynamics; (i) south of the Polar Front, (ii) northern Barents Sea shelf, and (iii) shelf slope and Arctic Ocean. During summer, high abundances of Atlantic/boreal and cosmopolitan zooplankton, mainly Calanus finmarchicus, Metridia longa, Oithona similis and Microsetella norvegica were found just south of the Polar Front in the central Barents Sea. On the shelf, Arctic species, such as Calanus glacialis, Pseudocalanus spp., and Limacina helicina dominated year-round with relatively high and stable biomass. At the northernmost stations, peaks of C. finmarchicus and Oncaeidae (Triconia borealis and Oncaea spp.) occurred in winter, combined with bathypelagic species such as Paraeuchaeta spp., Scaphocalanus brevicornis, Spinocalanus spp., Gaetanus brevispinus and Heterorhabdus norvegicus. Hence, when comparing the mesozooplankton communities at the different locations and seasons, four distinct communities were identified: shelf winter, shelf spring, shelf summer, and Arctic Ocean. Stronger advection and increased northward expansion of Atlantic zooplankton species are anticipated in the future, which could impact the diversity of the more endemic and energy-richer Arctic zooplankton communities.

Spatially heterogeneous habitat use across distinct biogeographic regions in a wide-ranging predator, the Persian leopard

Spatially heterogeneous habitat use across distinct biogeographic regions in a wide-ranging predator, the Persian leopard

The Skin Microbiome: Current Landscape and Future Opportunities

Our skin is the largest organ of the body, serving as an important barrier against the harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this barrier protects the body from invading pathogens through a sophisticated innate immune response and co-adapted consortium of commensal microorganisms, collectively termed the microbiota. These microorganisms inhabit distinct biogeographical regions dictated by skin physiology. Thus, it follows that perturbations to normal skin homeostasis, as occurs with ageing, diabetes and skin disease, can cause microbial dysbiosis and increase infection risk. In this review, we discuss emerging concepts in skin microbiome research, highlighting pertinent links between skin ageing, the microbiome and cutaneous repair. Moreover, we address gaps in current knowledge and highlight key areas requiring further exploration. Future advances in this field could revolutionise the way we treat microbial dysbiosis associated with skin ageing and other pathologies.

The latitudinal gradient in plant community assembly processes: Ameta-analysis.

Beta(β)-diversity, or site-to-site variation in species composition, generally decreases with increasing latitude, and the underlying processes driving this pattern have been challenging to elucidate because the signals of community assembly processes are scale-dependent. In this meta-analysis, by synthesising the results of 103studies that were distributed globally and conducted at various spatial scales, we revealed a latitudinal gradient in the detectable assembly processes of vascular plant communities. Variations in plant community composition at low and high latitudes were mainly explained by geographic variables, suggesting that distance decay and dispersal limitations causing spatial aggregation are influential in these regions. In contrast, variation in species composition correlated most strongly with environmental variables at mid-latitudes (20-30°), reflecting the importance of environmental filtering, although this unimodal pattern was not statistically significant. Importantly, our analysis revealed the effects of different spatial scales, such that the correlation with spatial variables was stronger at smaller sampling extents, and environmental variables were more influential at larger sampling extents. We concluded that plant communities are driven by different community assembly processes in distinct biogeographical regions, suggesting that the latitudinal gradient of biodiversity is created by a combination of multiple processes that vary with environmental and species size differences.

Mycobiota of Eucommia ulmoides bark: Diversity, rare biosphere and core taxa

Bark represents a unique microbial habitat. Revealing the interactions among bark-associated microbes is important for understanding their diversity, stability, and function, and how core microbiome influences the health and production of the host plant. We used amplicon sequencing of bark from the medicinal plant Eucommia ulmoides collected across nine distinct biogeographical regions in China, and comprehensively analyzed the diversity, rare biosphere and core taxa of bark fungi. The co-occurrence network results showed significant differences in the compositions of core mycobiota in E. ulmoides bark between the nine regions. Ecological factors (e.g., temperature and rainfall) were crucial determinants of differences in the unique core mycobiota of E. ulmoides from different regions. The metacommunity-scale network indicated that Cladosporium , Alternaria , and Teratosphaeria were core fungal taxa of E. ulmoides bark. Moreover, some core fungal taxa included rare taxa in particular local communities which, despite their relatively low abundance, may play a significant role in the community structure of E. ulmoides bark. • Rare taxa were a critical part of fungal community of E. ulmoides bark. • The composition of core microbiota was various among the different regions. • Cladosporium , Alternaria and Teratosphaeria were core taxa in metacommunity network.

The Effect of Seed Size on Germination and Seedling Growth in Sweet Chestnut (Castanea sativa Mill.)

The quantity and quality of seedlings in the nursery has an impact on the success of re-establishment and later growth. High germination rates enable a sufficient number of seedlings, and their quality is assessed using a number of parameters, including seedling height and root collar diameter. These parameters are influenced in some species by seed size, but the correlation between them is species-specific. The model species in this research was sweet chestnut (Castaneasativa Mill.), and seeds from 12 populations from two distinct biogeographical regions of Croatia were collected. We examined the influence of seed size on four parameters: germination rate, seedling height, root collar diameter and sturdiness quotient. Seed size has been shown to have a positive influence on both seedling height and root collar diameter, whereas no such correlation was noted for germination rate and sturdiness quotient. Significant differences in nut size and seedling growth parameters were found between the Mediterranean and continental populations, with higher values observed in the coastal Mediterranean populations. We concluded that seed origin and seed size have a significant impact on seedling growth and are important factors to consider when choosing seed material. Further nursery operations should consider seed origin and local environmental conditions when choosing seedlings for reforestation efforts and general forest operations.

Phylogeographic analysis of Thyrsites atun (Perciformes: Gempylidae) reveals connectivity between fish from South Africa and Chile

ABSTRACT The snoek, Thyrsites atun, is a pelagic fish of the family Gempylidae that inhabits cold waters of the southern hemisphere. It is an important fishing resource species (e.g. Chile, Namibia, New Zealand) linked mainly to the artisanal fisheries, however, its phylogeographic and population aspects are largely unknown. In this study we provide the first detailed analysis of the phylogeographic patterns and demographic processes of the snoek for the southern hemisphere using mitochondrial data of the Cytochrome c Oxidase subunit I gene. Our results indicate two lineages: (i) Australia-New Zealand, and (ii) Chile-South Africa-Namibia. The Australia-New Zealand clade shows partial isolation between populations associated with distinct biogeographic regions, likely driven by the region’s oceanography. The divergence between the lineages happened ∼800,000 years ago. On the other hand, analysis of the fish caught in the South-eastern Pacific (Chile) showed that the genetic diversity among localities (hT = 0.657) was lower than within localities (hS = 0.664), which was consistent with the pairwise comparisons results, suggesting the absence of phylogeographic structure. Based on our estimations, population expansion in T. atun would have occurred ∼7.5 ka (after LGM) under the Bayesian skyline plots approximation. We discuss the scope that this study could have in fisheries management of this important species.

Transcriptome of weeping pinyon pine, Pinus pinceana, shows differences across heterogeneous habitats

We reconstructed the needle tissue Transcriptome of P. pinceana for individuals from distinct biogeographic regions across a temperature and precipitation gradient that represents its natural distribution. Gene expression analysis via RNA-Seq identified differential response to biotic stress. Phenotypic plasticity includes physiological traits affected by subtle changes in mRNA expression levels, causing different molecular phenotypes. We assessed the differential response to climate heterogeneity across the geographic range of Pinus pinceana G. Gordon & Glendinning. This pinyon pine shows a fragmented geographic distribution suggesting adaptation to the arid and extreme conditions of the eastern mountain slopes of the Chihuahuan desert. The geographic distribution of P. pinceana spans regions with significant variation in annual temperature and precipitation. We tested whether phenotypic divergence is supported by differences in expression profiles in P. pinceana mature trees along its natural distribution and corresponds to the changes in drought and other environmental stress. The reconstructed Transcriptome included 45,431 high-quality annotations derived from the needles of seven individuals across contrasting biogeographic and climatic localities. Trees from the driest regions shared active responses related to abiotic factors. The differential expression analysis identified intermediates and regulators of abiotic stress response for 26 genes, highlighting families involved in the environmental response to abiotic stress, and proteins linked to up-regulated responses, such as LRR receptor-like serine/threonine-protein kinase and L-type lectin receptor kinases (LecRK), directly related to pathogens. When Chihuahuan desert samples were compared with arboretum samples, we found differential expression of a regulator of root morphogenesis, cysteine-rich receptor-like protein kinase (CRK28), which could relate to differential absorption in drought conditions.

Contrasting responses of native ant communities to invasion by an ant invader, Linepithema humile

Invasive alien species pose a serious threat to the integrity and function of natural ecosystems. Understanding how these invaders alter natural communities is therefore an important aspect in predicting the likely future outcomes of biological invasions. Many studies have documented the consequences of invasive alien species on native community structure, through the displacement and local extinction of native species. However, sampling methods and intensities are rarely standardised across such studies, meaning that it is not clear whether differences in response among native communities to the same invader species are due to biological differences between the invaded regions, or differences in the methodologies used. Here we use a matched sampling methodology to compare the effects of the Argentine ant (Linepithema humile Mayr) on native ant community assemblages in two distinct biogeographical regions that share similar ecologies: Girona (Spain) and Jonkershoek Nature Reserve (South Africa). We found a strong negative association between L. humile presence and native ant species richness within both geographic regions. However, the effects differed between the two study regions: in Girona, a single native ant species (Plagiolepis pygmaea) persisted in invaded sites; by contrast, substantially more native ant species persisted at invaded sites in Jonkershoek Nature Reserve. In addition, in Jonkershoek Nature Reserve, the abundance of certain native species appeared to increase in the presence of L. humile. This study therefore demonstrates the potential variable effects of an invasive species in contrasting locations within different biogeographical regions. Future work should explore the causes of this differential resistance among communities and expand standardised sampling approaches to more invaded zones to further explore how local biotic or abiotic conditions of a region determine the nature and extent of impact of L. humile invasion on native ant communities.

Response Surface Methodology Optimization and Kinetics of Diesel Degradation by a Cold-Adapted Antarctic Bacterium, Arthrobacter sp. Strain AQ5-05

Petroleum hydrocarbons, notably diesel oil, are the main energy source for running amenities in the Antarctic region and are the major cause of pollution in this area. Diesel oil spills are one of the major challenges facing management of the Antarctic environment. Bioremediation using bacteria can be an effective and eco-friendly approach for their remediation. However, since the introduction of non-native organisms, including microorganisms, into the Antarctic or between the distinct biogeographical regions within the continent is not permitted under the Antarctic Treaty, it is crucial to discover native oil-degrading, psychrotolerant microorganisms that can be used in diesel bioremediation. The primary aim of the current study is to optimize the conditions for growth and diesel degradation activity of an Antarctic local bacterium, Arthrobacter sp. strain AQ5-05, using the Plackett-Burman approach and response surface method (RSM) via a central composite design (CCD) approach. Based on this approach, temperature, pH, and salinity were calculated to be optimum at 16.30 °C, pH 7.67 and 1.12% (w/v), respectively. A second order polynomial regression model very accurately represented the experimental figures’ interpretation. These optimized environmental conditions increased diesel degradation from 34.5% (at 10 °C, pH 7.00 and 1.00% (w/v) salinity) to 56.4%. Further investigation of the kinetics of diesel reduction by strain AQ5-05 revealed that the Teissier model had the lowest RMSE and AICC values. The calculated values for the Teissier constants of maximal growth rate, half-saturation rate constant for the maximal growth, and half inhibition constants (μmax, Ks, and Ki), were 0.999 h−1, 1.971% (v/v) and 1.764% (v/v), respectively. The data obtained therefore confirmed the potential application of this cold-tolerant strain in the bioremediation of diesel-contaminated Antarctic soils at low temperature.

The Effect of Plant Geographical Location and Developmental Stage on Root-Associated Microbiomes of Gymnadenia conopsea.

Gymnadenia conopsea (L.) R. Br. is an important perennial terrestrial photosynthetic orchid species whose microbiomes are considered to play an important role in helping its germination and growth. However, the assemblage of G. conopsea root-associated microbial communities is poorly understood. The compositions of fungal and bacterial communities from the roots and corresponding soil samples in G. conopsea across distinct biogeographical regions from two significantly different altitudes were characterized at the vegetative and reproductive growth stages. The geographical location, developmental stage and compartment were factors contributing to microbiome variation in G. conopsea. Predominant fungal taxa include Ascomycota, Basidiomycota, Mortierellomycota and Chytridiomycota, whereas Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Verrucomicrobia, Chloroflexi, TM7 and Planctomycetes were predominant bacterial taxa. Using G. conopsea as a model, the structural and functional composition in G. conopsea root-associated microbiomes were comprehensive analyzed. Contrary to previous studies, biogeography was the main factor influencing the microbial community in this study. Besides, compartment and developmental stage should also be considered to analyze the variation of microbiota composition. Although the microbial composition varied greatly by location, the symbiotic microorganisms of G. conopsea still have certain specificity. This study gives an abundant information of G. conopsea root-associated microbiomes and provides new clues to better understanding the factors affecting the composition and diversity of fungal/bacterial communities associated with orchids. Our results also laying a foundation for harnessing the microbiome for sustainable G. conopsea cultivation. Moreover, these results might be generally applicable to other orchidaceae plants.

Influence of life-history-dependent migration strategies on Atlantic salmon diets

AbstractMigratory behaviour may vary according to the life history and demographic attributes of fish and lead to the spatial segregation of distinct population segments during the non-breeding season. In adult Atlantic salmon, spawning history differences are associated with intra-population variation in marine movements, but the degree of connectivity in spatial resource use among and within maiden and repeat spawning salmon is not well understood. We analysed muscle fatty acids (FAs), δ13C and δ15N of Atlantic salmon returning to spawn, and found significant differences among spawning histories. Maiden and alternate repeat spawning Atlantic salmon were differentiated from consecutive repeat spawners by fatty acid biomarkers associated with distinct biogeographic regions of the Labrador Sea, consistent with differential migration and divergent feeding locations. The presence and pattern of feeding contrasts among spawning history groups were further supported by dorsal muscle δ15N, which covaried with FA compositional values and distinguished consecutive repeat spawners from the two other groups. Because the degree of connectivity among population segments affects the ecological factors faced by such groups, an improved understanding of differential migration is necessary to better predict potential population responses to environmental change.

Extending Janzen’s hypothesis to temperate regions: A test using subterranean ecosystems

Abstract Janzen’s hypothesis (1967; American Naturalist) predicts that tropical habitats with reduced thermal seasonality would select for species with narrow thermal tolerance, thereby limiting dispersal among sites of different elevations showing little overlap in temperature. These predictions have so far been tested by confronting tropical and temperate mountain communities, leaving unresolved the question of their generalization to habitats with low thermal seasonality outside the tropics. We provide the first extension of Janzen’s hypothesis to temperate habitats, by testing for differences in thermal tolerance and elevational range among congeneric alpine spiders (Araneae: Linyphiidae: Troglohyphantes) occurring along a steep gradient of decreasing thermal seasonality with increasing cave depth. Using species from the same temperate region rather than from distinct biogeographic regions avoids confounding the effects of short‐ and long‐term climatic variability on thermal tolerance and elevational range extent. Following Jansen’s assumptions, we predicted that cave habitats with low thermal seasonality would select for narrow thermal tolerance. Also, specialized subterranean species would exhibit both narrower elevational range extents and smaller realized thermal niche breadths. Initially, we showed that thermal seasonality and the overlap in temperature across caves were considerably lower in deep than in shallow cave habitats. Then, we measured thermal tolerance and used morphological traits to quantify the degree of specialization to subterranean life of 11 spider species. We found that thermal tolerance decreased with increasing subterranean specialization. Deep subterranean species reached their critical temperature at 1–4°C above their habitat temperature, whereas shallow subterranean species withstood a twofold larger temperature increase. At last, we demonstrated that a species’ elevational range extent and the variation of temperature encountered across its range decreased with increasing specialization to deep subterranean life. Our integrative work, being grounded in organismal and habitat measures, represents the first generalization of Janzen’s framework to caves and provides a conceptual framework to disentangle the effect of long‐term climate variability on subterranean biodiversity patterns. Extending Janzen’s thoughts to a broader range of ecosystems is key to understanding how the ecological specialization–dispersal trade‐off may constrain the response of species to climate change. A free Plain Language Summary can be found within the Supporting Information of this article.

Front Cover: Distinguishing three distinct biogeographic regions with an in‐house developed 39‐AIM‐InDel panel and further admixture proportion estimation for Uyghurs

Front Cover: Distinguishing three distinct biogeographic regions with an in‐house developed 39‐AIM‐InDel panel and further admixture proportion estimation for Uyghurs

Molecular operational taxonomic units reveal restricted geographic ranges and regional endemism in the Indo‐Pacific octocoral family Xeniidae

AbstractAimTo quantify taxon diversity, biogeographic distributions and patterns of community assembly in xeniid octocorals using molecular operational taxonomic units (MOTUs).LocationRed Sea, Indian and western Pacific Oceans.TaxonXeniidae, a family of reef‐dwelling octocorals (Anthozoa, Octocorallia).MethodsXeniids collected at 13 locations were sequenced at three barcode loci, and assigned to MOTUs defined by minimum genetic distance thresholds. Taxon richness (number of MOTUs) and endemicity (per cent of MOTUs found at a single location) were quantified. Patterns of β‐diversity (species turnover) and phylogenetic β‐diversity (lineage turnover) among geographical regions were visualized using hierarchical clustering, non‐metric multidimensional scaling (NMDS) plots and distance‐decay relationships. Community assembly was investigated by comparing the mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) separating species in each assemblage to values generated for null communities.ResultsA genetic distance threshold of 0.3% discriminated 67 MOTUs, with taxon richness ranging from 2–18 MOTUs per site. Out of the 67 MOTUs, 48 (72%) were found at only a single location, and only two spanned both the western Indian and Pacific Oceans. Species turnover among sites was high, but phylogenetic β‐diversity was lower than β‐diversity and differed significantly from null models of community assembly at only two sites. β‐diversity and phylogenetic β‐diversity both increased significantly with geographic distance, and sites clustered into three distinct biogeographic regions (Red Sea and western Indian Ocean; Western Australia; western Pacific Ocean and Great Barrier Reef, Australia). All five major clades of xeniids were represented in each region.Main conclusionsA genetic approach to biodiversity estimation suggests that most xeniid taxa are regional endemics whose geographic distribution is likely governed by dispersal limitation. This conclusion contrasts with published records of certain morphospecies occurrences, which imply that they have broad geographic ranges. So far, the distribution of xeniid biodiversity mirrors that of scleractinian corals, with species richness highest in the Coral Triangle, but endemicity peaking in peripheral areas.

Distinguishing three distinct biogeographic regions with an in-house developed 39-AIM-InDel panel and further admixture proportion estimation for Uyghurs.

In the forensic field, ancestry-informative markers (AIMs) showing remarkable allele frequency discrepancies can be useful in deducing the likely ancestral origin of a person or estimating the ancestry component proportions of an admixed population or individual. Diallelic single nucleotide polymorphisms are genetic markers commonly used for ancestry inference, but the genotyping methods of single nucleotide polymorphisms fail to fulfil the demands of cost-effectiveness and simplicity of experimental manipulation. To overcome the limitations, a 39 ancestry-informative insertion/deletion polymorphism multiplex panel was developed in the present study to perform ancestry assignment of individuals from three distinct biogeographic regions (Africa, Europe, East Asia). And in the panel design, we also attempted to incorporate AIM-insertion/deletion polymorphisms exhibiting allelic frequency differences in Han, Uyghur, and Tibetan populations into the multiplex assay, further expecting to provide valuable information for refining ancestry inference within Chinese populations. Statistical analyses were performed to estimate efficiency of this panel in clustering individuals from three continents mentioned above into their corresponding populations, which indicated the potential of the panel in ancestry inference. Besides, we also estimated the ancestral component proportions of Uyghur group and STRUCTURE analysis revealed that Uyghurs from Urumchi city of northern Xinjiang exhibited a distinctly admixed pattern of East Asian and European ancestry components with a ratio of 49:44, reflecting the relatively higher East Asian ancestry component contribution in the gene pool of the Uyghur group.

The structure and function of the global citrus rhizosphere microbiome

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.

Biological and physical controls on the oxygen cycle in the Kuroshio Extension from an array of profiling floats

The Kuroshio Extension (KE) is a current associated with the largest CO2 flux into the Pacific Ocean, a broad region of uptake that extends across the Pacific basin between the subarctic and subtropical regions. The relative importance of the biological and physical processes controlling this sink is uncertain. Because oxygen is stoichiometrically linked to changes in dissolved inorganic carbon due to photosynthesis and respiration and subject to many of the same physical drivers as the CO2 flux, in situ oxygen measurements help to determine the processes driving this large CO2 flux. We analyzed data from eight Argo profiling floats equipped with oxygen sensors to estimate oxygen fluxes in the upper ocean of the KE region (approximate bounds: 25°N to 45°N, 135°E to 155°E). In situ air calibrations of these sensors allowed us to accurately measure air-sea oxygen differences, which largely control the flux of oxygen to and from the atmosphere. To characterize distinct biogeographical regions in the Kuroshio Extension and to accommodate seasonal north-south shifts in the location of the regional boundaries, we averaged oxygen measurements from different floats along isopycnal surfaces into 3 regions based on temperature-salinity relationships: North KE, Central KE, and South KE. Using these regional concentration time series, we determined the physical fluxes using an upper ocean layered model and calculated the residual oxygen flux, a combination of column-integrated net community production and physical processes unexplained by the model. The annual oxygen budget is largely a balance of air-sea exchange and the residual oxygen term. Residual oxygen fluxes are -5.4 ± 1.1, -5.9 ± 0.1, and 2.1 ± 2.2 mol O2 m-2 yr-1 (where negative is a loss from the upper ocean) for the North, Central, and South KE regions, respectively. The North and Central KE are regions of mode water formation, which balances the large air-sea fluxes into the ocean. The South KE oxygen residual indicates a biologically produced flux to the atmosphere in two out of three years that agrees with previous estimates of subtropical annual net community production (ANCP) but exhibits high interannual variability. This study suggests that physical processes are the primary drivers for the annual uptake of the gases oxygen and carbon dioxide in the Central KE region where the annual CO2 uptake is strongest.