Determining Community Composition Research Articles

The Emu Bay Shale: A unique early Cambrian Lagerstätte from a tectonically active basin.

The Emu Bay Shale (EBS) of South Australia is anomalous among Cambrian Lagerstätten because it captures anatomical information that is rare in Burgess Shale-type fossils, and because of its inferred nearshore setting, the nature of which has remained controversial. Intensive study, combining outcrop and borehole data with a compilation of >25,000 fossil specimens, reveals that the EBS biota inhabited a fan delta complex within a tectonically active basin. Preservation of soft-bodied organisms in this setting is unexpected and further underscores differences between the EBS and other Cambrian Lagerstätten. Environmental conditions, including oxygen fluctuations, slope instability, high suspended sediment concentrations, and episodic high-energy events, inhibited colonization of the lower prodelta by all but a few specialist species but favored downslope transportation and preservation of other largely endemic, shallow-water benthos. The EBS provides extraordinary insight into early Cambrian animal diversity from Gondwana. These results demonstrate how environmental factors determined community composition and provide a framework for understanding this unique Konservat-Lagerstätte.

Spatio-temporal dynamics in microalgal communities in Arctic land-fast sea ice

Sea ice microalgae are an important source of energy for the polar marine food web, representing the primary carbon source prior to pelagic phytoplankton blooms. Here we investigate community dynamics of sea ice microalgal communities in land-fast sea ice across six different fjords in high-Arctic Svalbard, Norway, during Spring (April – May). We found that light (0.1 – 23% incoming PAR / 0.1 – 193 μmol photons m-2s-1) played a central role in determining community composition, with more diverse assemblages observed in sites with more light transmitted to the bottom ice community. In April, microalgal assemblages were similar when under-ice light transmittance was similar, independent of geographical location, however this light-derived separation of community structure was not evident in May. At all sites, assemblages were dominated by pennate diatoms, with the most abundant taxon being Nitzschia frigida. However, with increasing under-ice light transmittance, we saw an increase in the relative abundance of Dinophyceae, Navicula spp. and Thalassiosira spp.. A positive relationship between light and δ13C enrichment and C:N ratios in the ice algal biomass demonstrated the effect of light on the biochemical composition of ice algae. Light did not correlate with cell abundance or chlorophyll a concentration. With anticipated changes to Arctic sea ice extent and snow cover as a result of climate change, we will see shifts in the light transmitted to the bottom ice community. These shifts, whether caused by reduced light transmittance from increased snow cover or increased light transmittance from thinning ice, snow depth or increased rainfall, will likely alter sea ice microalgal community composition, which in turn, may influence the success of secondary production and biogeochemical cycling in polar waters.

Thresholds of seascape fauna composition along gradients of human pressures and natural conditions to inform marine spatial planning

Knowledge about the cumulative impacts of anthropogenic activities and environmental conditions on marine ecosystems is incomplete and details are lacking. Compositional community changes can occur along gradients, and community data can be used to assess the state of community resilience against combined impacts of variables representing human pressures and environmental conditions. Here we use a machine learning approach, i.e., Gradient Forest, to identify explanatory variable thresholds and select relevant epibenthic fauna and demersal fish species, which can be used to inform an integrated management of multiple human pressures and conservation planning in the southern North Sea. We show that a broad selection of anthropogenic and environmental variables, such as natural disturbance of the seafloor and euphotic depth, determined community composition thresholds of 67 epibenthic fauna and 39 demersal fish species along environmental conditions and human pressure gradients in the southern North Sea between 2010 and 2020. This has the potential to inform resilience assessments under the Marine Strategy Framework Directive to promote and retain a good environmental status of marine ecosystems.

Community assembly processes and drivers shaping marine fish community structure in the North Sea

To preserve natural ecosystems and their biodiversity, there is a need to anticipate future ecosystem changes through better understanding of underlying drivers and assembly processes determining community composition. Assembly processes can be understood as a set of filters acting at different spatio‐temporal scales that jointly define the structure and composition of communities. Here, we explore the underlying assembly processes shaping marine fish species distribution and composition, using the heavily exploited North Sea. Our aims are to study 1) the relative importance of the different assembly processes shaping marine fish communities, 2) the key environmental drivers determining species distributions and composition, and to 3) quantify the role of traits in determining species niches and responses to the environment. Specifically, we fit a joint species distribution model (JSDM) using 31 years of standardized scientific bottom trawl survey data for 67 fish species. We use a set of environmental variables and species' traits representing morphology, life history, reproduction and diet, while also accounting for phylogenetic relationships of species. Environmental variables, primarily related to temperature, explained over one third of the variance in species occurrence, while spatial effects explained half of the variability across species. This shows that environmental filtering and spatially‐structured processes are the main drivers shaping the community assembly. Furthermore, among the total variance of individual species occurrences, 12.5% could be explained by traits, which improve the mechanistic understanding on species responses to environmental change. Hence, model predictions from JSDMs accounting for traits, environmental niches and potential interactions among multiple species can provide relevant simulations and forecasts with the potential to inform spatial management and conservation efforts aiming to preserve biodiversity and its associated services vital for human well‐being.

Linking agricultural diversification practices, soil arthropod communities and soil health

Abstract Soil arthropods comprise a substantial portion of soil biodiversity and regulate processes in the soil ecosystem. Despite this, cropping system diversification designed to improve soil health for agriculture is rarely evaluated for its effects on soil arthropod biodiversity and community structure. As a result, soil arthropods are not usually considered in management decisions. To address this gap, we evaluated the effects of agricultural diversification through rotation on soil arthropods and soil properties using replicated large‐plot field studies representing two climatically distinct agroecological classes (AECs) in the dryland cereal‐growing region of the inland Pacific Northwest, USA. We investigated how different 3‐year annual crop rotations affected soil arthropod biodiversity and community structure. Treatments reflected ‘business‐as‐usual’ rotations in dryland systems and diversified rotations achieved by incorporating novel winter pea (WP) or forage crops (FORs). We also assessed relationships between the Soil Biological Quality index (QBS‐ar), which uses soil arthropods as bioindicators of soil health, and other biological and physiochemical soil health indicators. We collected 710 community samples with 82,509 arthropod specimens across 66 taxa. Novel crops in diversified rotations promoted soil arthropod abundance and biodiversity relative to crops they could replace in rotation. Crop type determined community composition. Most taxa driving differences in community structure were predators and detritivores associated with WP and FORs. In addition to effects on soil arthropods associated with specific crops, effects were also detected across rotations. Incorporating WP into rotations improved QBS‐ar across entire rotations, not just in the WP phases, in both AECs. Links between QBS‐ar and other soil health indicators were complex and varied by AEC. Synthesis and applications: Soil arthropods respond to agricultural diversification and can be used as bioindicators to assess the effects of diversification on soil health. Below‐ground arthropod communities are structured by crop type, suggesting that planting specific crops may promote soil arthropods and their services. We showed that incorporating winter pea and forage crops into dryland cereal rotations supported soil arthropod biodiversity and soil health. Results indicate that soil arthropod assessments can be included in the soil health framework to guide agricultural management decisions.

Comparing anesthetic stations and environmental DNA sampling to determine community composition of cryptobenthic coral reef fishes of Vava’u, Kingdom of Tonga

Comparing anesthetic stations and environmental DNA sampling to determine community composition of cryptobenthic coral reef fishes of Vava’u, Kingdom of Tonga

Diversity and Community Structure of Typhlocybinae in the Typical Karst Rocky Ecosystem, Southwest China

In karst ecosystems, different geographic environmental conditions can lead to different lithospheric conditions, thus determining community composition and altering biotic interactions. Guizhou Province is a typical ecologically fragile karst area located in the South China Karst. To explore the relationship between biodiversity and environmental changes in different karst habitats, the community structure of typhlocybinae (Hemiptera, Auchenorrhyncha, and Cicadellidae) in three typical karst areas in Guizhou Province (the Zhenfeng–Huajiang Demonstration Zone, the Bijie Salaxi Demonstration Zone, and the Shibing Yuntai Mountain Nature Reserve) was analyzed. These areas are characterized by differences in terms of their geographic environment. For field investigations, typhlocybinae specimens were collected from five common leafhopper host plants—Juglans regia L., Rhus chinensis Mill., Prunus persica (L.) Batsch, Prunus salicina Lindl., and Debregeasia orientalis C.J. Chen—in the three study areas. A total of 4078 typhlocybinae specimens were captured, belonging to 6 tribes, 40 genera, and 121 species. Among them, Alnetoidia dujuanensis, Limassolla lingchuanensis, and Singapora shinshana were the dominant species. The numbers of typhlocybinae specimens from each region were as follows: Shibing, 2170 (53.2%); Bijie, 973 (23.9%); and Huajiang, 935 (22.9%). The number of leafhoppers collected in areas with serious rocky desertification was low, and the number increased with the increase in vegetation coverage. The order of the influence of environmental factors on the community structure of the leafhoppers in the three study areas was Huajiang > Bijie > Shibing. This order is consistent with the ranking of rocky desertification grades in the three study areas. The order based on the number of units at different taxonomic levels was as follows: Bijie (6 tribes, 32 genera, and 68 species) > Huajiang (6 tribes, 22 genera, and 58 species) > Shibing (5 tribes, 21 genera, and 48 species). The results show that environmental factors, such as climate and host plant leaf traits, had various effects on the characteristics and diversity of the leafhopper communities in different grades of rocky desertification areas. This study demonstrates that there are differences in species diversity in different grades of karst rocky desertification areas and provides a theoretical basis for future rocky desertification control and regional ecological restoration.

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

Most biological diversity on Earth is contained within microbial communities. In the ocean, these communities dominate processes related to carbon fixation and nutrient recycling. Yet, specific factors that determine community composition and metabolic activity are difficult to resolve in complex microbial populations, complicating predictions of microbial processes in a changing ocean. Microbial metabolism generates small organic molecules that reflect both the biochemical and physiological diversity as well as the taxonomic specificity of these biological processes. These small molecules serve as the conduit for taxon-specific signaling and exchange. Here, we use liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to taxonomically categorize 111 metabolites that include small molecules in central and secondary metabolism across 42 taxa representing numerically dominant and metabolically important lineages of microbial autotrophs and heterotrophs. Patterns in metabolite presence-absence broadly reflected taxonomic lineages. A subset of metabolites that includes osmolytes, sulfur-containing metabolites, sugars, and amino acid derivatives provided chemotaxonomic information among phytoplankton taxa. A variety of phytohormones and signaling molecules were predominantly found in the heterotrophic bacteria and archaea, expanding knowledge of metabolites implicated in modulating interactions between microbes. This chemotaxonomic inventory of marine microbial metabolites is a key step in deciphering metabolic networks that influence ocean biogeochemical cycles.

Xylella fastidiosa Infection Reshapes Microbial Composition and Network Associations in the Xylem of Almond Trees.

Xylella fastidiosa represents a major threat to important crops worldwide including almond, citrus, grapevine, and olives. Nowadays, there are no efficient control measures for X. fastidiosa, and the use of preventive measures and host resistance represent the most practical disease management strategies. Research on vessel-associated microorganisms is gaining special interest as an innate natural defense of plants to cope against infection by xylem-inhabiting pathogens. The objective of this research has been to characterize, by next-generation sequencing (NGS) analysis, the microbial communities residing in the xylem sap of almond trees affected by almond leaf scorch disease (ALSD) in a recent X. fastidiosa outbreak occurring in Alicante province, Spain. We also determined community composition changes and network associations occurring between xylem-inhabiting microbial communities and X. fastidiosa. For that, a total of 91 trees with or without ALSD symptoms were selected from a total of eight representative orchards located in five municipalities within the X. fastidiosa-demarcated area. X. fastidiosa infection in each tree was verified by quantitative polymerase chain reaction (qPCR) analysis, with 54% of the trees being tested X. fastidiosa-positive. Globally, Xylella (27.4%), Sphingomonas (13.9%), and Hymenobacter (12.7%) were the most abundant bacterial genera, whereas Diplodia (30.18%), a member of the family Didymellaceae (10.7%), and Aureobasidium (9.9%) were the most predominant fungal taxa. Furthermore, principal coordinate analysis (PCoA) of Bray–Curtis and weighted UniFrac distances differentiated almond xylem bacterial communities mainly according to X. fastidiosa infection, in contrast to fungal community structure that was not closely related to the presence of the pathogen. Similar results were obtained when X. fastidiosa reads were removed from the bacterial data set although the effect was less pronounced. Co-occurrence network analysis revealed negative associations among four amplicon sequence variants (ASVs) assigned to X. fastidiosa with different bacterial ASVs belonging to 1174-901-12, Abditibacterium, Sphingomonas, Methylobacterium–Methylorubrum, Modestobacter, Xylophilus, and a non-identified member of the family Solirubrobacteraceae. Determination of the close-fitting associations between xylem-inhabiting microorganisms and X. fastidiosa may help to reveal specific microbial players associated with the suppression of ALSD under high X. fastidiosa inoculum pressure. These identified microorganisms would be good candidates to be tested in planta, to produce almond plants more resilient to X. fastidiosa infection when inoculated by endotherapy, contributing to suppress ALSD.

A temporal refuge from predation can change the outcome of prey species competition

Generalist predators whose primary prey undergoes cyclic fluctuations, will predate on alternate food sources when the abundance of their primary prey is low. In this paper we have developed a general model of a predator that switches predation between its primary prey and two alternative, competing, prey species. When the predators primary prey is at high abundance, predation of the alternate, competing, prey species is low, which provides periods of temporal refuge for the alternate prey from predation. When the inter‐specific interactions between the competing prey species lead to different dynamical outcomes in the presence and absence of predation, increasing the duration of the temporal refuge promotes dominance of a competitively superior species that is vulnerable to predation. The general theoretical framework was extended to consider a key case study system of pine marten predation on red and grey squirrels. In the absence of predation, grey squirrels out‐compete red squirrels but preferential predation by pine marten on grey squirrels can suppress grey squirrel density and allow red squirrel recovery. A temporal refuge for both squirrel species can arise due to prey switching by pine marten in years when field voles, their primary prey in the UK, are abundant. The duration of the temporal refuge, quantified as the relative length of the multi‐annual vole population cycle where vole density is above a population threshold, is a critical factor determining the persistence of red and grey squirrels. Our findings therefore provide insights for the conservation of the endangered red squirrel in the UK and the Republic of Ireland and more generally on the influence of the population dynamics of primary prey species in determining community composition.

Elevation and Soil Properties Determine Community Composition, but Not Vascular Plant Richness in Tropical Andean Roadside

Roadsides are common ecosystems worldwide, with specific environmental characteristics and multiple effects on plant diversity. As such, they represent examples of highly dynamic anthropogenic ecosystems. Our objective was to assess patterns of vascular species diversity in response to elevation and soil characteristics on a roadside in the Andean mountains of Ecuador. The study area was located in the southern Ecuadorian Andes, at five elevations ± 400 m a.s.l. (2600, 2200, 1800, 1400 and 1000 m a.s.l.), where we recorded species richness and abundance in transects perpendicular to the road. The effects of elevation and soil characteristics on species abundance and richness were analyzed using generalized linear mixed models (GLMMs), while species composition was assessed with a non-metric multidimensional scaling analysis (NMDS) and its relationship to environmental variables. We used indicator species analyses (ISA) to identify which species significantly characterized specific elevation and soil factors from primary succession for restoration processes at the roadside. Although elevation and soil characteristics do not condition vascular species richness, the composition is more similar at elevations E1 and E2 (2600 m and 2200 m a.s.l.), differing from low elevations E4 and E5 (1400 m and 1000 m a.s.l.), which in turn are more similar to each other, while intermediate elevation E3 is similar to the highest and lowest elevations. Soil variables that limited plant communities were pH, bulk density (gr/cm3), silt (%), and sand (%) contents. The indicator species showed a preference for specific environmental and soil condition requirements associated with the different microhabitats and, thus, can be suggested for potential use in roadside revegetation processes in tropical areas. These results can help decision-makers in the implementation of biodiversity conservation and roadside environmental restoration projects in areas of Andean mountain ecosystems which have been affected by the construction of road infrastructure.

Variation in biotic interactions mediates the effects of masting and rainfall fluctuations on seedling demography in a subtropical rainforest

Abstract Seedling dynamics are critical for determining community composition and future forest structure. Two mechanisms are crucial drivers of seedling vital rates: biotic interactions and environmental filtering. Biotic interactions at the neighbourhood scale, such as the Janzen–Connell effect, are considered among the main mechanisms maintaining species coexistence. These effects can show considerable temporal variation because of changes in neighbourhood density (i.e. seedling recruitment following masting years) and weather conditions. However, there is limited evidence of whether interannual variation in these conditions modulates biotic interactions and its potential cascading effects on seedling vital rates. We used seedling data collected over 17 years in a subtropical rainforest in northern Taiwan. We modelled interannual variation in first‐year survival and growth of 12,830 seedlings of 36 species and 47 cohorts using (generalized) linear mixed‐effects models with several crowding indices and abiotic conditions (edaphic and topographic factors) as predictors. The first‐year seedling survival and growth depended on both weather conditions and neighbourhood density. Seedling survival was greater when recruitment was more abundant and in years with greater rainfall, and this was mostly mediated by the interaction with conspecific and heterospecific seedlings. Seedling growth decreased with the increasing abundance of new recruits and increased with annual rainfall. Growth was negatively affected by the basal area of conspecific and heterospecific trees and by the density of conspecific seedlings when the number of new recruits was greater. The abiotic factors had a limited effect on seedling survival and growth compared to biotic factors. Synthesis. Our results show that variation in recruitment abundance due to masting and annual rainfall significantly affects seedling vital rates by changing biotic interactions. These findings are in accordance with the economy of scale hypothesis, which predicts higher per‐capita reproductive success in years of higher seed production. Furthermore, the results support the hypothesis that fluctuations in rainfall can alter biotic interactions in forests. Efforts to predict forest community responses to climate changes should consider the temporal variations in biotic interactions.

Impact of Lagrangian Sea Surface Temperature Variability on Southern Ocean Phytoplankton Community Growth Rates

AbstractOcean phytoplankton play a critical role in the global carbon cycle, contributing ∼50% of global photosynthesis. As planktonic organisms, phytoplankton encounter significant environmental variability as they are advected throughout the ocean. How this variability impacts phytoplankton growth rates and population dynamics remains unclear. Here, we systematically investigated the impact of different rates and magnitudes of sea surface temperature (SST) variability on phytoplankton community growth rates using surface drifter observations from the Southern Ocean (>30°S) and a phenotype‐based ecosystem model. Short‐term SST variability (<7 days) had a minimal impact on phytoplankton community growth rates. Moderate SST changes of 3–4°C over 7–45 days produced a large time lag between the temperature change and the biological response. The impact of SST variability on community growth rates was nonlinear and a function of the rate and magnitude of change. Additionally, the nature of variability generated in a Lagrangian reference frame (following trajectories of surface water parcels) was larger than that within an Eulerian reference frame (fixed point), which initiated different phytoplankton responses between the two reference frames. Finally, we found that these dynamics were not captured by the Eppley growth model commonly used in global biogeochemical models and resulted in an overestimation of community growth rates, particularly in dynamic, strong frontal regions of the Southern Ocean. This work demonstrates that the timescale for environmental selection (community replacement) is a critical factor in determining community composition and takes a first step towards including the impact of variability and biological response times into biogeochemical models.

Commercial fish abundance estimation in the Belgian part of the North Sea through eDNA ddPCR analyses

Monitoring of fish assemblages in the Belgian part of the North Sea (BPNS) mainly happens through trawling. While effective, this method is invasive and destructive as it disturbs bottom communities, catches non-target species and removes organisms from the environment. A more sustainable alternative for monitoring marine diversity is the use of environmental DNA (eDNA) which comprises intra- and extracellular genetic material that comes from the shedding of organic material, like scales and mucus in the case of fish. When applying metabarcoding on eDNA, community composition can be inferred simply by analysing a small volume of water. Therefore the technique does not disturb the environment, and the high sensitivity of eDNA allows the detection of rare and transient species that are frequently missed by traditional sampling methods. Next to determining community composition, the amount of eDNA copies in the water could potentially be used to quantify target fish species in the marine environment. Here, we investigate whether eDNA concentrations from marine water samples correlate with local fish abundance estimates obtained via traditional beam trawling. Species specific Droplet Digital Polymerase Chain Reaction (ddPCR) assays were designed and tested for three economically important species: common sole (Solea solea), plaice (Pleuronectes platessa) and whiting (Merlangius merlangus). In march 2020, 12 sites in the BPNS were selected based on absence, low and high abundances of the three target species as observed in epibenthos monitoring data from previous years. In each site, 2L of seawater was collected with a niskin bottle from ca 1m above the sea floor. Subsequently, beam trawl transects of 1 km were conducted and all epibenthos species caught in the trawling net were morphologically identified, counted and weighted. Our results indicate promising correlations between eDNA concentrations obtained with the ddPCR assays and the number of specimens in the net for all three species. Some “false” positive results were obtained with the ddPCR, but these may actually be “true” positive detections because the fish might be present in the area but were not caught in the trawling transects. This warrants further investigation to see how far eDNA signals can be detected in the North Sea system. Next, 50 water samples were collected in Autumn 2020, involving more locations with or without the three fishes. This time samples were taken at the beginning, middle and end of the 1 km transects to investigate small scale horizontal variation in eDNA concentrations. The autumn samples are currently being processed. In March 2021, samples will be taken at different depths (surface, middle of the water column and ca 1m above the seafloor) to investigate whether there are any vertical patterns in eDNA distribution in a very well mixed system such as the BPNS. A DNA shedding experiment will be performed as well to estimate the rate at which the three fishes shed DNA. This will provide important information on how quickly fishes can be detected when they swim by. The information obtained with the field sampling and experimental setting will help to strengthen the correlation to a point that reliable abundance estimations of our target species become possible and will allow us to evaluate the potential of eDNA as a sustainable alternative/addition to traditional monitoring methods.

Tree Species Richness and Neighborhood Effects on Ectomycorrhizal Fungal Richness and Community Structure in Boreal Forest.

Tree species identity is one of the key factors driving ectomycorrhizal (EcM) fungal richness and community composition in boreal and temperate forest ecosystems, but little is known about the influence of tree species combinations and their neighborhood effects on EcM communities. To advance our understanding of host plant effects on EcM fungi, the roots of silver birch, Scots pine, and Norway spruce were analyzed using high-throughput sequencing across mature boreal forest exploratory plots of monocultures and two- and three-species mixtures in Finland. Our analyses revealed that tree species identity was an important determinant of EcM fungal community composition, but tree species richness had no significant influence on EcM fungal richness and community composition. We found that EcM fungal community composition associated with spruce depends on neighboring tree species. Our study suggests that at a regional-scale tree species identity is the primary factor determining community composition of root-associated EcM fungi alongside with tree species composition effects on EcM fungal community of spruce in mixed stands.

Tropical mammal functional diversity increases with productivity but decreases with anthropogenic disturbance.

A variety of factors can affect the biodiversity of tropical mammal communities, but their relative importance and directionality remain uncertain. Previous global investigations of mammal functional diversity have relied on range maps instead of observational data to determine community composition. We test the effects of species pools, habitat heterogeneity, primary productivity and human disturbance on the functional diversity (dispersion and richness) of mammal communities using the largest standardized tropical forest camera trap monitoring system, the Tropical Ecology Assessment and Monitoring (TEAM) Network. We use occupancy values derived from the camera trap data to calculate occupancy-weighted functional diversity and use Bayesian generalized linear regression to determine the effects of multiple predictors. Mammal community functional dispersion increased with primary productivity, while functional richness decreased with human-induced local extinctions and was significantly lower in Madagascar than other tropical regions. The significant positive relationship between functional dispersion and productivity was evident only when functional dispersion was weighted by species' occupancies. Thus, observational data from standardized monitoring can reveal the drivers of mammal communities in ways that are not readily apparent from range map-based studies. The positive association between occupancy-weighted functional dispersion of tropical forest mammal communities and primary productivity suggests that unique functional traits may be more beneficial in more productive ecosystems and may allow species to persist at higher abundances.

Environmental and Management Control over the Submontane Grassland Plant Communities in Central Slovakia

In Central Europe, submontane grassland plant biodiversity is currently threatened by management intensification as well as by the cessation and abandonment of management activities (extensive grazing and mowing). Although the vegetation of Central European grasslands has been well described by phytosociological papers, there is still a need to improve our understanding of the effect of both management and environment on species richness and community composition. We studied submontane grassland communities in Central Slovakia. Our study showed that both environmental variables and management were important for shaping the submontane grassland species richness and floristic composition. Plant species richness showed a weak negative relationship with soil pH. When grassland management types were analyzed individually, the amount of phosphorus, nitrogen, pH, and altitude were all found to be significantly correlated with plant species richness or diversity. Management type and local environmental factors (i.e., incoming solar radiation) both determined community composition.

Development of fluorescence in situ hybridization (FISH) probes to detect and enumerate Gambierdiscus species

Ciguatera poisoning (CP) is a syndrome caused by the bioaccumulation of lipophilic ciguatoxins in coral reef fish and invertebrates, and their subsequent consumption by humans. These phycotoxins are produced by Gambierdiscus spp., tropical epiphytic dinoflagellates that live on a variety of macrophytes, as well as on dead corals and sand. Recent taxonomic studies have identified novel diversity within the Gambierdiscus genus, with at least 18 species and several sub-groups now identified, many of which co-occur and differ significantly in toxicity. The ability to accurately and quickly distinguish Gambierdiscus species in field samples and determine community composition and abundance is central to assessing CP risk, yet most Gambierdiscus species are indistinguishable using light microscopy, and other enumeration methods are semi-quantitative. In order to investigate the spatial and temporal dynamics of Gambierdiscus species and community toxicity, new tools for species identification and enumeration in field samples are needed. Here, fluorescence in situ hybridization (FISH) probes were designed for seven species commonly found in the Caribbean Sea and Pacific Ocean, permitting their enumeration in field samples using epifluorescence microscopy. This technique enables the assessment of community composition and accurate determination of cell abundances of individual species. Molecular probes detecting G. australes, G. belizeanus, G. caribaeus, G. carolinianus, G. carpenteri, and the G. silvae/G. polynesiensis clade were designed using alignments of large subunit ribosomal RNA (rRNA) sequences. These probes were tested for specificity and cross-reactivity through experiments in which field samples were spiked with known concentrations of Gambierdiscus cultures, and analyzed to confirm that Gambierdiscus can be successfully detected and enumerated by FISH in the presence of detritus and other organisms. These probes were then used to characterize Gambierdiscus community structure in field samples collected from the Florida Keys and Hawai‘i, USA. The probes revealed the co-occurrence of multiple species at each location. Time-series FISH analyses of samples collected from the Florida Keys quantified seasonal shifts in community composition as well as fluctuations in overall Gambierdiscus cell abundance. Application of species-specific FISH probes provides a powerful new tool to those seeking to target individual Gambierdiscus species, including significant toxin-producers, in field populations. Moving forward, analysis of Gambierdiscus community composition across multiple environments and over time will also allow species dynamics to be linked to environmental parameters, improving our ability to understand and manage the current and changing risks of CP worldwide.

Consistent and transient drivers of freshwater zooplankton communities

AbstractAimInferences of the predominant processes that structure communities are commonly based on single ‘snapshots’ in time, which may miss temporally transient but important mechanisms. In this study, we compared key environmental and spatial drivers of zooplankton composition across multiple years to quantify shifts in their relative importance through time, and to identify any drivers of temporal change.LocationSouthern Ontario, Canada.TaxonZooplankton.MethodsZooplankton were collected from 29 lakes in southern Ontario, Canada over four years (2013–2016). Variation partitioning was used to quantify the relative importance of independent and covarying components of local environmental conditions, regional east‐west and north‐south compositional trends, and inter‐lake geographic distance in each year. Measured environmental metrics included aspects of lake morphology and chemistry, and spatial relationships were quantified using lake latitude/longitude coordinates and Moran's Eigenvector Maps (MEMs). Redundancy analyses (RDAs) were also used to compare the influence of individual environmental and spatial variables across years.ResultsMost local‐scale and regional‐scale community processes were consistently important across all surveyed years, but some were less consistent. Specifically, geomorphology was always an important driver of local environmental and regional spatial community patterns. This occurred because local community composition was strongly affected by whether a lake was shallower versus deeper, and due to spatial clusters of shallow and deep lakes that produced negative spatial autocorrelation in community composition. Conversely, the individual influences of lake chemistry and spatial east‐west compositional trends were important in some years and not in others, potentially due to inter‐annual shifts in the predominant environmental variables and extreme weather events.Main conclusionsA single‐year community snapshot can provide insight into consistent or slowly changing community structuring processes, such as those driven by geomorphology, but may not completely capture temporally transient mechanisms. Furthermore, snapshots collected during anomalous seasons or years may misrepresent which mechanisms are predominantly determining community composition. Future efforts to understand local and regional community drivers would therefore benefit from considering which processes are likely temporally ‘consistent’ versus ‘transient’, and studies with more variable components would benefit from considering or controlling for temporal shifts in their importance.

The conundrum of biont-free substrates on a high-energy continental shelf: Burial and scour on Nantucket Shoals, Great South Channel

A survey of the adjacent waters east of Nantucket, Massachusetts provided an opportunity to evaluate the epibiota attached to cobbles, rocks, boulders, and Atlantic surfclam shell in a region of high tidal current velocity and sand scour where burial, exhumation, and scour may limit epibiont coverage on exposed, and thus otherwise highly preferred for attachment, substrates. Such conditions may confute the expectation that substrate complexity always adds significantly to ecosystem value by expanding the range of habitat options and consequently increasing species richness and trophic linkages. Sedimentary particles potentially providing good attachment substrate for erect sessile epibiota included surfclam shells, abundant at many locations, cobbles, nearly ubiquitous, rocks, routinely encountered, and occasional boulders. The attached epibiota fell into three categories based on their biases for particle types. Some preferred the largest particles or evidence of their occupation was best preserved on these particles: these included sponges, mussels, and barnacles and their scars. Some preferred intermediate and smaller terrigenous particles; these included tunicates and encrusting bryozoans. Some preferred surfclam shells, namely the slipper shells and erect hydroids. Slow-growing attached epibionts were exceedingly rare and all soft-bodied attached epibionts were rare. Only barnacles and their taphonomic scars and hydroids were common. The frequency of barnacle scars relative to intact barnacles suggests sediment scour under a high-flow regime. Mussels were rarely attached to larger sedimentary particles such as cobbles and rocks, though commonly occurring locally as mussel beds on sand and pebble, further supporting the ephemerality of exposed unscoured attachment sites. The absence of attached epibionts demonstrates that edaphic processes minimize the importance of cobbles, rocks, boulders, and shells in community structure in some subtidal high-energy regimes, defying expectations from their contribution to substrate complexity. Their apparent contribution to habitat complexity belies their resultant much more minor role in determining community composition, thereby limiting their ecosystem value.