High‐throughput sequencing reveals neustonic and planktonic microbial eukaryote diversity in coastal waters

Neustonic organisms inhabit the sea surface microlayer (SML) and have important roles in marine ecosystem functioning. Here, we use high‐throughput 18S rRNA gene sequencing to characterize protist and fungal diversity in the SML at a coastal time‐series station and compare with underlying plankton assemblages. Protist diversity was higher in February (pre‐bloom) compared to April (spring bloom), and was lower in the neuston than in the plankton. Major protist groups, including Stramenopiles and Alveolata, dominated both neuston and plankton assemblages. Chrysophytes and diatoms were enriched in the neuston in April, with diatoms showing distinct changes in community composition between the sampling periods. Pezizomycetes dominated planktonic fungi assemblages, whereas fungal diversity in the neuston was more varied. This is the first study to utilize a molecular‐based approach to characterize neustonic protist and fungal assemblages, and provides the most comprehensive diversity assessment to date of this ecosystem. Variability in the SML microeukaryote assemblage structure has potential implications for biogeochemical and food web processes at the air‐sea interface.     

Seasonal strengths of the abiotic and biotic drivers of a zooplankton community

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Effects of temperature variability on community structure in a natural microbial food web

Climate change research has demonstrated that changing temperatures will have an effect on community‐level dynamics by altering species survival rates, shifting species distributions, and ultimately, creating mismatches in community interactions. However, most of this work has focused on increasing temperature, and still little is known about how the variation in temperature extremes will affect community dynamics. We used the model aquatic community held within the leaves of the carnivorous plant, Sarracenia purpurea, to test how food web dynamics will be affected by high temperature variation. We tested the community response of the first (bacterial density), second (protist diversity and composition), and third trophic level (predator mortality), and measured community respiration. We collected early and late successional stage inquiline communities from S. purpurea from two North American and two European sites with similar average July temperature. We then created a common garden experiment in which replicates of these communities underwent either high or normal daily temperature variation, with the average temperature equal among treatments. We found an impact of temperature variation on the first two, but not on the third trophic level. For bacteria in the high‐variation treatment, density experienced an initial boost in growth but then decreased quickly through time. For protists in the high‐variation treatment, alpha‐diversity decreased faster than in the normal‐variation treatment, beta‐diversity increased only in the European sites, and protist community composition tended to diverge more in the late successional stage. The mortality of the predatory mosquito larvae was unaffected by temperature variation. Community respiration was lower in the high‐variation treatment, indicating a lower ecosystem functioning. Our results highlight clear impacts of temperature variation. A more mechanistic understanding of the effects that temperature, and especially temperature variation, will have on community dynamics is still greatly needed.     

Seasonal flow variation allows 'time-sharing' by disparate aquatic insect communities in montane desert streams

1. Flow variation can drive major abiotic changes in stream environments between seasons. Theoretically, disparate biotic communities could be maintained during different seasons at a single site if suitable refuges and colonist sources were available. Using isolated montane desert streams in south‐east Arizona as a model system, we hypothesised that two disparate aquatic insect faunas (montane temperate and neotropical) could be maintained at the same sites through strong seasonal variation in abiotic conditions. 2. We collected aquatic insects representing 59 families from seven streams during high‐flow (March–April) and low‐flow (June) sampling periods across two years. We assessed changes in aquatic insect community and functional feeding group composition by habitat (riffle, pool) and season (high flow, low flow). 3. Within sites, wetted stream area decreased by an average of 97% between high‐flow (predominately riffles) and low‐flow (predominately pools) seasons. Community composition likewise showed strong seasonal patterns; the montane temperate fauna was strongly associated with the high‐flow season while neotropical hemipterans and coleopterans were associated with the low‐flow season. Increased water temperature was significantly associated with this shift from temperate to neotropical assemblages. 4. Functional feeding group composition shifted dramatically by season. The proportion of predators increased from 24.5% (high flow) to 75.2% (low flow) while collector–filterers and shredders declined from 38.4% (high flow) to 1.7% (low flow). 5. We suggest that habitat ‘time‐sharing’ by disparate communities is facilitated via strong seasonal variation in temperature and flow and the presence of high elevation refuges or diapause stages for temperate montane taxa to survive the dry season.     

Comparison of different denaturing gradient gel electrophoresis primer sets for the study of marine bacterioplankton communities

An annual seasonal cycle of composition of a bacterioplankton community in an oligotrophic coastal system was studied by denaturing gradient gel electrophoresis (DGGE) using five different primer sets. Analysis of DGGE fingerprints showed that primer set 357fGC-907rM grouped samples according to seasons. Additionally, we used the set of 16S rRNA genes archived in the RDPII database to check the percentage of perfect matches of each primer for the most abundant bacterial groups inhabiting coastal plankton communities. Overall, primer set 357fGC-907rM was the most suitable for the routine use of PCR-DGGE analyses in this environment.     

Comparison of Different Denaturing Gradient Gel Electrophoresis Primer Sets for the Study of Marine Bacterioplankton Communities

An annual seasonal cycle of composition of a bacterioplankton community in an oligotrophic coastal system was studied by denaturing gradient gel electrophoresis (DGGE) using five different primer sets. Analysis of DGGE fingerprints showed that primer set 357fGC-907rM grouped samples according to seasons. Additionally, we used the set of 16S rRNA genes archived in the RDPII database to check the percentage of perfect matches of each primer for the most abundant bacterial groups inhabiting coastal plankton communities. Overall, primer set 357fGC-907rM was the most suitable for the routine use of PCR-DGGE analyses in this environment.     

Closely related protist strains have different grazing impacts on natural bacterial communities

Heterotrophic protists are abundant in most environments and exert a strong top‐down control on bacterial communities. However, little is known about how selective most protists are with respect to their bacterial prey. We conducted feeding trials using cercomonad and glissomonad Cercozoa by assaying them on a standardized, diverse bacterial community washed from beech leaf litter. For each of the nine protist strains assayed here, we measured several phenotypic traits (cell volume, speed, plasticity and protist cell density) that we anticipated would be important for their feeding ecology. We also estimated the genetic relatedness of the strains based on the 18S rRNA gene. We found that the nine protist strains had significantly different impacts on both the abundance and the composition of the bacterial communities. Both the phylogenetic distance between protist strains and differences in protist strain traits were important in explaining variation in the bacterial communities. Of the morphological traits that we investigated, protist cell volume and morphological plasticity (the extent to which cells showed amoeboid cell shape flexibility) were most important in determining bacterial community composition. The results demonstrate that closely related and morphologically similar protist species can have different impacts on their prey base.     

Between‐individual variation drives the seasonal dynamics in the trophic niche of a Neotropical marsupial

The dynamics of population niches result from the variation in resource use within individuals and also from the variation between individuals. The prevalence of one mechanism or the other leads to competing hypotheses about the major mechanisms underlying the empirical observations of the contraction/expansion dynamics of the trophic niche in natural populations. In this study, we investigated how within‐ and between‐individual variation in resource use shapes the food niche dynamics of the woolly mouse opossum, Marmosa paraguayana (Didelphimorphia: Didelphidae), in a remnant of the highly seasonal Cerrado in south‐eastern Brazil. To do so, we analysed the faecal samples of live‐trapped individuals to determine their diets within the wet and dry seasons. In addition to a seasonal shift in the composition of the diet, the population trophic niche was significantly wider during the dry season than the wet season. This expansion resulted from larger between‐individual variation in the dry season that was not related to sex preferences, whereas the individual niche widths did not significantly increase from the wet to the dry seasons. Our findings add to the growing list of animal populations that show individual‐level variation in resource use. Furthermore, these results represent a pattern of individual‐level response to seasonal changes that is different from patterns reported for other organisms. We suggest that a pathway to build more realistic foraging models and produce more accurate predictions on population and community dynamics is to consider between‐individual variation and short‐term niche dynamics.     

Bird diversity patterns in Neotropical temperate farmlands: The role of environmental factors and trophic groups in the spring and autumn

Productivity, habitat heterogeneity and environmental similarity are of the most widely accepted hypotheses to explain spatial patterns of species richness and species composition similarity. Environmental factors may exhibit seasonal changes affecting species distributions. We explored possible changes in spatial patterns of bird species richness and species composition similarity. Feeding habits are likely to have a major influence in bird–environment associations and, given that food availability shows seasonal changes in temperate climates, we expect those associations to differ by trophic group (insectivores or granivores). We surveyed birds and estimated environmental variables along line‐transects covering an E‐W gradient of annual precipitation in the Pampas of Argentina during the autumn and the spring. We examined responses of bird species richness to spatial changes in habitat productivity and heterogeneity using regression analyses, and explored potential differences between seasons of those responses. Furthermore, we used Mantel tests to examine the relationship between species composition similarity and both the environmental similarity between sites and the geographic distance between sites, also assessing differences between seasons in those relationships. Richness of insectivorous birds was directly related to primary productivity in both seasons, whereas richness of seed‐eaters showed a positive association with habitat heterogeneity during the spring. Species composition similarity between assemblages was correlated with both productivity similarity and geographic proximity during the autumn and the spring, except for insectivore assemblages. Diversity within main trophic groups seemed to reflect differences in their spatial patterns as a response to changes between seasons in the spatial patterns of food resources. Our findings suggest that considering different seasons and functional groups in the analyses of diversity spatial pattern could contribute to better understand the determinants of biological diversity in temperate climates.     

Long-term seasonal variation in the biological traits of benthic-macroinvertebrates in two Mediterranean-climate streams in California, U.S.A.

1. We investigated the seasonal variation of biological traits and the influence of interannual rainfall variability on this pattern. Using long‐term survey data (6–19 years) from an intermittent and a perennial stream in the Mediterranean‐climate region of northern California, we examined 16 fuzzy‐coded biological traits (e.g. maximum size, life cycle duration, and mode of respiration). 2. Seasonal habitat variability is higher in the intermittent stream than in the perennial stream. During the winter and spring wet‐season both streams flood; however, during the summer dry‐season, the intermittent stream forms isolated pools in (occasionally drying completely). 3. Seasonal habitat variability influenced both taxonomic and biological trait composition. Distinct taxonomic communities were present in each season, particularly in the intermittent stream. The intermittent stream also exhibited more seasonal variation in biological traits than the perennial stream. 4. Despite statistically significant seasonal variation, trait composition was relatively stable among seasons in comparison with taxonomic composition and abundance. Taxonomic composition varied considerably between seasons, because of high seasonal and interannual replacement of taxa resulting from seasonal habitat changes. 5. The seasonality of taxonomic composition and abundance was sensitive to interannual rainfall variability. In dry years, the taxonomic composition of communities was more similar between seasons than in wet years, while trait composition was relatively insensitive to rainfall variability. 6. Despite high seasonal variation in abundance and taxonomic composition, biological traits of aquatic macroinvertebrates varied less and exhibited seasonal stability, which may be a result of the unpredictability and harshness of stream environments.     

Dynamics of Invertebrate Benthic Communities and Drift in a Regulated River of Central Spain

We document invertebrate benthic and drift dynamics in a regulated river in central Spain at two temporal scales: seasonal (for both benthos and drift) and daily (for drift). The benthic abundance of individuals and taxon richness generally increased in the summer. Drift abundance showed no seasonal or daily variation, but taxon richness of drifting individuals was higher in the spring. Both ben‐thos and drift showed clear seasonal changes in taxonomic composition. Interestingly, some benthic taxa showed their highest abundances in the spring, while others were more abundant in the summer. In contrast, most drifting taxa were more abundant in the spring. Different functional feeding groups showed different patterns of variation throughout the year, both in the benthos and the drift. Daily variations in drift were present in very few taxa and functional feeding groups, and only in some seasons. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Temporal stability vs. community matrix measures of stability and the role of weak interactions

Relationships between different measures of stability are not well understood in part because empiricists and theoreticians tend to measure different aspects and most studies only explore a single form of stability. Using time‐series data from experimental plankton communities, we compared temporal stability typically measured by empiricists (coefficient of variation in biomass) to stability measures typically measured by theoreticians derived from the community matrix (asymptotic resilience, initial resilience and intrinsic stochastic invariability) using first‐order multivariate autoregressive models (MAR). Community matrices were also used to derive estimates of interaction strengths between plankton groups. We found no relationship between temporal stability and stability measures derived from the community matrix. Weaker interaction strengths were generally associated with higher stability for community matrix measures of stability, but were not consistently associated with higher temporal stability. Temporal stability and stability measures derived from the community matrix stability appear to represent different aspects of stability reflecting the multi‐dimensionality of stability.     

A functional perspective for breeding and wintering waterbird communities: temporal trends in species and trait diversity

Waterbird communities are prone to strong temporal changes both seasonally and annually, but little is known about how this affects their functional diversity and community assembly. Detecting temporal trends in taxonomic and functional diversity within (alpha diversity) and between (beta diversity) communities in breeding and wintering seasons could give insight into the ecological processes driving those trends. In this study, we investigated trends in wintering and breeding waterbirds within and between eleven wetlands in Mediterranean Spain, using a 28‐year time‐series up to 2017. We assessed the temporal trends in taxonomic and functional diversity measures, and compared observed functional diversity values with null expectations, in order to explore the mechanisms driving community assembly. We found increases over time in species richness and in the occupied functional space for both wintering and breeding communities, indicating that species with distinct functional roles were added in both seasons. However, the distribution of the abundances in the functional space was different for breeding and wintering communities. Dissimilarity of species and functional traits decreased among wetlands, suggesting that some of the same functional traits were added to the different wetlands, increasing regional homogenization through time. This is reflected in increases over time in mean body mass, diet plasticity and in the importance of fish in waterbird diets, plus declines in the dietary importance of invertebrates and in plasticity of feeding strata. Furthermore, species composition between wintering and breeding communities, but not trait composition, has become more similar through time. Our results highlight that annual changes, and especially seasonal changes, in the composition of waterbird communities have different effects on their functional diversity, and are influenced by opposing community assembly mechanisms.     

马鞍列岛岩礁生境鱼类群落结构时空格局

基于2009年马鞍列岛潮下带岩礁生境的多网目三层组合刺网逐月调查数据,对鱼类群落月相和季度间的变化、区域尺度上的空间差异和群落的稳态进行了探讨,应用优势种相对丰度和生物量、定居性鱼类和洄游种的季节动态、非度量多维标度(nMDS)和生物量丰度曲线(ABC)分析方法对群落时空格局进行了分析。结果显示:季节性洄游种集中出现在夏秋季,但对岩礁生境的利用表现出不同区域的强度差异;小黄鱼Larimichthys polyactis和黄姑鱼Nibea albiflora周年利用岩礁生境,但强度有别,尤其在冬季;定居性鱼类褐菖鲉Sebastiscus marmoratus、斑头鱼Agrammus agrammus和大泷六线鱼Hexagrammos otakii在春末夏初的种群密度最高,同样表现出某些或大部分月份的区域差异;而河口种中国花鲈Lateolabrax maculatus则更多地选择秋冬季出现在岩礁生境。多元分析结果揭示了当地岩礁生境鱼类群落格局上显著的季节和区域差异,这是定居性鱼类对岩礁生境利用的阶段性变化和区域差异、结合洄游种季节迁移和选择性分布等因素作用下共同形成的格局。ABC分析进一步发现,丰富的鱼类生态类型形成了夏季岩礁生境更为稳定的群落状态,而冬季相反;同时各季度A区的群落干扰明显强过B区。研究表明,产卵季节海域西北部的岩礁生境很可能起着主要的产卵场功能,而东南部区域各季度皆侧重于幼鱼育肥场的功能表达。丰富的种类区系加之优势种的季节性交替出现,共同塑造了岩礁生境极具动态的鱼类群落格局,对维持岛礁海域鱼类多样性以及局部区域生态系统的稳定性起着非常重要的作用。     

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land‐cover change affects belowground carbon storage and nutrient availability. We measured intra‐ and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well‐replicated, long‐term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter‐ and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land‐use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities.     

Assemblage structure and dynamics of terrestrial birds in the southwest Amazon: a camera‐trap case study

Habitat spatial distribution, seasonal variation, and activity patterns influence changes in vertebrate assemblages over time. Terrestrial birds play major roles in the dynamics of tropical forests, but there are few effective methods to study these species due to their cryptic coloration and elusive behavior. We used camera‐trap data collected during 16 mo (February 2017–June 2018) to describe the terrestrial avifauna in southeastern Peru, assess to what extent the composition of terrestrial avifauna changes among seasons and across two major habitats (terra firme and floodplain forests), and determine daily activity patterns of terrestrial birds. We used overlap analyses to examine temporal co‐occurrence between ecologically similar and sympatric species. Camera traps recorded 16 species, including eight species in the family Tinamidae. Capture rates were highest for Pale‐winged Trumpeters (Psophia leucoptera; Psophiidae) and Gray‐fronted Doves (Leptolila rufaxilla; Columbidae). Species composition did not differ between habitats or seasons, and capture rates between habitats only differed for White‐throated Tinamous (Tinamus guttatus). Overlaps of activity patterns were high between ecologically similar species and species found in terra firme habitats (White‐throated Tinamous and Cinereous Tinamous, Crypturellus cinereus) and in both habitat types (Pale‐winged Trumpeters and Gray‐fronted Doves). Low numbers of captures of possibly locally rare or less abundant species hindered a complete analysis of spatial and seasonal patterns of terrestrial bird assemblages. We suggest a greater sampling effort and greater spatial replication to better understand the spatial and seasonal dynamics of the terrestrial avifauna. Further studies that assess the mechanisms that allow the coexistence of sympatric tinamous would be valuable, both in our study area and elsewhere. The use of camera traps in long‐term monitoring projects proved to be an effective tool for monitoring terrestrial birds, identifying cryptic and often rare animals to species level, and providing valuable ecological information at species and community levels.     

How do different aspects of biodiversity change through time? A case study on an Australian bird community

The study of ecological communities through time can reveal fundamental ecological processes and is key to understanding how natural and human pressures will affect biodiversity. Most studies of ecological communities through time consider only one or a few summary measures (e.g. species richness, total abundance), which might neglect important aspects of community structure or function. We studied temporal variation in several measures of species diversity, size diversity, and species composition in an intensively sampled bird community to determine whether different biodiversity measures change synchronously. We used a novel function regression model, which supports the study of diversity measures that are distributions (e.g. species abundance distributions) alongside measures that are scalar values (e.g. species richness). Most diversity measures changed predictably within years, but inter‐annual changes in size diversity and species composition were not reflected in species diversity. Within and among years, there was considerable variation in distributional measures that was not captured in scalar measures. Predictable variation within years probably was related to seasonal variation in weather patterns or food availability, but variation in size diversity among years probably resulted from stochastic changes in species composition. These results suggest that species and size diversity may be decoupled, and that inferences on scalar diversity measures might not reflect fundamental changes to community structure or function. Our method supports the inclusion of size‐based measures and distributional measures in ecological analyses, and broader uptake of our approach is likely to provide new insight into the processes structuring ecological communities, and inform the links between structure and function in ecological communities.     

Seasonal trophic dynamics affect zooplankton community variability

1. The degree to which communities are variable may be affected by the ecological conditions to which they are exposed and can affect their propensity to form alternative states. We examined the influence of two common ecological factors, predation and seasonal successional stage, on the variability in community composition of herbivorous pond plankton. In a highly replicated, two factor, mesocosm experiment we determined whether beta diversity was affected by seasonal successional stage of the community (two levels), by fish predation (presence/absence) or by their interaction. 2. Several significant changes were found in the composition of the rotifer, cladoceran and copepod assemblages. Most cladoceran abundances showed sharp declines in the presence of fish, while some rotifers, as well as their assemblage species richness, responded favourably to fish. The copepod assemblage was composed of omnivorous and carnivorous species, which added invertebrate predation to the experiment and which intensified as the season progressed. Copepods showed responses to fish predation that depended on seasonal successional stage of the initial community, because of changes in their stage structure and edibility as they grew from nauplii to adults. 3. Community variability was consistently high at the end of each month‐long experimental period for both cladoceran and rotifer assemblages, except under two conditions. In the early season treatments, the rotifer assemblages were more consistent (lower beta diversity) in the presence of fish. This was attributed to high population growth rates for rotifers under these ecological conditions because of reduced copepod predation on them through a trophic cascade from fish. Low community variability was also observed in the late season for rotifers when fish were excluded and, as a result, they were exposed to high invertebrate predation from cyclopoid copepods. 4. Results from the early season support theoretical predictions that when community size increases, variability in composition should decline because of an increase in competitive processes over stochastic ones. Late season results suggest that a second mechanism, specialist predation, can also reduce prey community variability. Our study demonstrates that plankton communities may be more predictable under certain trophic web configurations and challenges ecologists to find ways to incorporate such inherent variability into experiments and community theory.     

长江口及邻近海域浮游动物群落结构及季节变化

根据2006—2007年长江口及其邻近海域(29°30'N—32°30'N,120°00'E—127°30'E)150个站位4个季节的调查资料,对长江口海域浮游动物群落结构、种类组成、优势种及其季节变化进行研究。结果表明,长江口及其邻近海域浮游动物群落物种多样性丰富,四季共鉴定浮游动物460种,隶属7个门,246属,此外,另有54类浮游幼体。其中,桡足类是最优势类群,有193种,占41.96%;端足类为第二优势类群,有51种,占11.09%;水螅水母为第三优势类群,有34种,占7.39%。长江口及其邻近海域浮游动物的物种多样性呈现明显季节变化,其特征为:夏季(317种)秋季(309种)春季(230种)冬季(138种)。中华哲水蚤和百陶带箭虫为长江口及其邻近海域的四季优势种。长江口及其邻近海域浮游动物大体可划分为5种生态类群:近岸低盐类群、广温广盐类群、低温高盐类群、高温广盐类群和高温高盐类群。结合同步调查的水文和水化学数据,进行浮游动物群落丰度与环境因子的相关分析表明:盐度是影响长江口及其邻近海域的浮游动物群落丰度的主要环境因子。     

海南岛以南海域浮游植物群落特征研究

为掌握海南岛以南海域浮游植物群落特征, 1998–1999年对其进行了4个航次的现场调查。经显微镜检, 共鉴定出浮游植物290种(包括23个变种和5个变型)。在此基础上, 作者通过统计和聚类分析方法, 研究了这一区域浮游植物的物种组成、丰度变动和群落结构等特征。结果显示, 海南岛以南海域浮游植物物种丰富, 以硅藻门和甲藻门为主; 物种组成的时空差异显著。其优势种的暖水性、高盐性或广盐性特征明显。冷季以广温种小舟形藻(Navicula subminuscula)占优势, 随气温回升, 暖水性种类优势地位突出。不同季节浮游植物丰度差异小, 以硅藻门丰度占优势, 但与冷季相比, 暖季中甲藻门和蓝藻门丰度明显上升。4月和9月的高丰度中心位于西部海域北部湾湾口附近, 1月和12月则出现在中东部水域。聚类结果显示各浮游植物群落组分无明显的斑块分布特征。群落物种多样性表现为4月和9月高于1月和12月; 群落稳定性以12月份为最差; 中南部水域群落稳定性较差。总之, 海南岛以南海域浮游植物群落具独特的热带开阔海域生物区系特征。冷暖季群落特征有明显差异。海域水文条件对群落特征的影响复杂。