Zoosporic true fungi and heterotrophic straminipiles assemblages from soil of Brazilian Cerrado areas

The influence of seasonal fluctuations and environmental factors on the occurrence and distribution of zoosporic true fungi and heterotrophic straminipiles in terrestrial ecosystems is poorly understood. This contribution analyses the species composition, frequency, abundance and diversity of zoosporic true fungi and heterotrophic straminipiles assemblages from two areas of Cerrado in the State of São Paulo, Brazil. Samples of soil were collected at four dates during the rainy and dry seasons. Twenty-one abiotic factors were measured. The assemblages showed a high diversity and evenness and were represented by 30 taxa of Chytridiomycota and Oomycota. Some abiotic factors appeared to have influenced the patterns of distribution and occurrence of the taxa in different areas and/or seasons. Even so, the biotic factors (richness, diversity indices and evenness) and the Sorensen index showed high similarity between the assemblages.     

Spatial structure of fish assemblages in a tropical estuarine lagoon: combining multivariate and geostatistical techniques

The spatial structure and seasonal changes of estuarine fish assemblages in the Ciénaga Grande de Santa Marta (CGSM) were analysed based on four seasonal comprehensive surveys conducted in 1993-1994 and 1997. Geostatistical and multivariate techniques were used to: (a) determine seasonal changes in spatial distribution of the species richness, and (b) identify assemblages of estuarine fish and their relation to abiotic factors. Potential biotic interactions affecting the assemblage structure were also explored. A total of 11075 individuals representing 39 species were collected, with Eugerres plumieri, Diapterus rhombeus, Micropogonias furnieri, Mugil incilis, Cathorops spixii, Elops saurus and Anchovia clupeoides as dominant species between seasons. Spatial distribution of fish richness differed between rainy and dry seasons in each year, whereas species mapping showed spatial patchiness in 1993-1994 and gradients during 1997. Strong evidence of species saturation was found in all seasons, suggesting biotic interactions limiting species richness at a threshold density of ca. 50 ind./5000 m². Marine, marine-estuarine and freshwater species were classified in each season according to their capability to cope with salinity fluctuations. Associations defined by functional feeding guilds were also identified. Empirical and statistic evidence showed that fish assemblages differed between seasons within each year, and each assemblage was always dominated by a small number of species, notably E. plumieri in both years 1993-1994 and 1997. Between-season differences in fish assemblage structure in the CGSM seem to be driven by abiotic factors; however, evidence of species saturation could suggest the existence of density-dependent factors operating together.     

Cumulative annual dung beetle diversity in Mediterranean seasonal environments

Species diversity assessments should consider the dynamic nature of ecological communities, especially in highly seasonal ecosystems. Here we provide a comprehensive framework for analysing seasonal changes in species composition, richness and diversity in two local dung beetle (Coleoptera: Scarabaeoidea: Aphodiidae, Geotrupidae, and Scarabaeidae) communities from Western Tuscany (Italy), in the Mediterranean ecoregion. We test whether, in this highly seasonal region, cumulative annual diversity is an oversimplification of well differentiated seasonal communities. Data were obtained through repeated standardised samples collected regularly over an entire year. We clearly identify different summer and winter communities at each site based on species composition and abundance. Seasonal richness and diversity values are different from the cumulative annual values, as a consequence of beta diversity between seasons, and some dung beetle species are identified as idiosyncratic of each particular season. Both ecological (niche partitioning) and biogeographical factors are suggested as drivers of these temporal variations. Thus, because local inventories of fauna that include records over long time periods actually reflect situations where coexistence and interactions are unlikely to occur, highly seasonal sites must be viewed as having temporally differentiated communities in order to reach feasible and reliable baselines for local diversity assessments.     

Nearly a decade‐long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan,China)

Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long‐term variations of bacterioplankton communities in lake ecosystems remain poorly understood. Here we present nearly a decade‐long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform. We found strong repeatable seasonal diversity patterns in terms of both common (detected in more than 50% samples) and dominant (relative abundance >1%) bacterial taxa turnover. Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is a key environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern of bacterioplankton communities across the main lake areas within season was overwhelmed by their temporal variabilities. Phylogenetic analysis further indicated that 75%–82% of community turnover was governed by homogeneous selection due to consistent environmental conditions within seasons, suggesting that the microbial communities in Lake Donghu are mainly controlled by niche‐based processes. Therefore, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout different lake areas.     

台湾海峡浮游翼足类群聚之季节动态

本研究利用水产试验所研究船“水试一号”于2006年冬(1月)夏(7月)两季在台湾海峡海域进行水文探测及浮游动物采样, 以探讨浮游翼足类群聚组成与丰度之时空分布及其与水文环境的相关性。结果发现浮游翼足类夏季的丰度及多样性指数明显较冬季高, 而种类数则差异不大; 两季间优势种类组成相似但优势排名略有不同, 夏季主要优势种为棒笔帽螺(Creseis clava)、尖笔帽螺(C. acicula)和马蹄螔螺(Limacina trochiformis), 合占所有翼足类丰度的97%, 其中仅棒笔帽螺就占了总丰度的62%; 冬季主要优势种为胖螔螺(Limacina inflata), 占翼足类丰度的72%。翼足类丰度在空间上的分布亦有明显的季节差异, 夏季时以台湾海峡北部较高, 冬季则以南部较高。种类数与物种多样性指数则均以海峡南部较高。由水文站群分析及各站群生物及水文特征结果显示, 台湾海峡季节性水团的消长与翼足类群聚分布有十分密切的关联。     

Seasonal cycles,phylogenetic assembly,and functional diversity of orchid bee communities

Neotropical rainforests sustain some of the most diverse terrestrial communities on Earth. Euglossine (or orchid) bees are a diverse lineage of insect pollinators distributed throughout the American tropics, where they provide pollination services to a staggering diversity of flowering plant taxa. Elucidating the seasonal patterns of phylogenetic assembly and functional trait diversity of bee communities can shed new light into the mechanisms that govern the assembly of bee pollinator communities and the potential effects of declining bee populations. Male euglossine bees collect, store, and accumulate odoriferous compounds (perfumes) to subsequently use during courtship display. Thus, synthetic chemical baits can be used to attract and monitor euglossine bee populations. We conducted monthly censuses of orchid bees in three sites in the Magdalena valley of Colombia – a region where Central and South American biotas converge – to investigate the structure, diversity, and assembly of euglossine bee communities through time in relation to seasonal climatic cycles. In particular, we tested the hypothesis that phylogenetic community structure and functional trait diversity changed in response to seasonal rainfall fluctuations. All communities exhibited strong to moderate phylogenetic clustering throughout the year, with few pronounced bursts of phylogenetic overdispersion that coincided with the transition from wet‐to‐dry seasons. Despite the heterogeneous distribution of functional traits (e.g., body size, body mass, and proboscis length) and the observed seasonal fluctuations in phylogenetic diversity, we found that functional trait diversity, evenness, and divergence remained constant during all seasons in all communities. However, similar to the pattern observed with phylogenetic diversity, functional trait richness fluctuated markedly with rainfall in all sites. These results emphasize the importance of considering seasonal fluctuations in community assembly and provide a glimpse to the potential effects that climatic alterations may have on both pollinator communities and the ecosystem services they provide.     

Evidence of seasonal migration in a tropical subterranean vertebrate

Many animals undergo migrations that depend on a range of biotic or abiotic factors provoking daily, seasonal or annual movement of individuals and/or populations. Temperate amphibians frequently have their life cycles dominated by annual temperature fluctuations, but in the tropics it is often presumed that distinct rainy seasons will influence amphibians more than small changes in temperature. Here, we direct the seasonal changes in abundance hypothesis to a caecilian amphibian Boulengerula boulengeri found in monthly randomized quantitative surveys in the top 30 cm of soil. Meteorological data are used to interpret the significant changes found in relation to rainfall and temperature variables. Instead of the expected correlation of migration with rainfall, we find that frequency varies significantly and positively with temperature. In addition, data on the depth at which individual caecilians are collected suggest that animals undergo a vertical (rather than horizontal) migration within the soil. This is the first example of vertical migrations with temperature (as opposed to rainfall) of any tropical subterranean fauna. We discuss the possible influences that stimulate migration in this species (abiotic factors, feeding, reproduction and predation). The ecology of caecilians has lagged behind that of all other tetrapods, and this study has importance for future ecological studies, as well as biodiversity assessments and monitoring methodologies.     

Environmental drivers of α-diversity patterns in monsoonal tropical stream fish assemblages: a case study from tributaries of Narmada basin,India

Environmental factors, such as local physico-chemical water parameters, habitat-structural conditions, geography and human disturbances can have a profound impact on the structure and composition of biotic communities. This study investigates the relationship of these factors with fish diversity in medium to small streams in Central India and identifies the key determinants of species richness and diversity in habitats increasingly facing impacts of urban development. Data on fish diversity on eighteen sites, representative of undisturbed and disturbed aquatic habitats, located in the Narmada river basin were collected across different seasons over two years. Seasonal patterns of alpha diversity for this region were analysed and the effect of environmental drivers on seasonal patterns of alpha diversity were assessed. Analyses of species data revealed significant differences in diversity patterns across seasons for both species richness and Shannon diversity. Results of generalized linear mixed models showed that along with disturbance, altitude and substrate heterogeneity, dissolved oxygen, pH and stream width proved to be important environmental variables that predict species richness. Further, variations in pH, dissolved oxygen, temperature, stream width, stream depth and stream width heterogeneity were found to also predict Shannon diversity index. Our study revealed that seasonal changes across the year play a crucial role in shaping diversity patterns. This study is relevant as an important step in identifying roles of various ecological factors driving fish diversity in the region and towards developing long term management plans for critical catchment areas of major rivers in tropical systems.     

Soil Microbial Diversity in the Vicinity of Desert Shrubs

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0–10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon–Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.     

Ecology of the Major Periphytic Diatom Communities from the Mesta River,Bulgaria

Epilithon, epiphyton, epipelon, epipsammon and plocon diatom samples and water chemistry samples were collected bimonthly from 11 stations along the Mesta River, Bulgaria between December 1989 and April 1991. Principal component analysis (PCA), correlation, and dominance analysis were employed for describing the seasonal dynamics of diatom assemblages and estimating the correlation between diatom distribution and the physico-chemical parameters. All periphytic communities were compared by PCA, MANOVA and Fisher's LSD multiple comparison test. Ionic strength and eutrophication were the major abiotic factors affecting diatom distribution in the epilithon, epiphyton, epipelon and epipsammon. Current velocity had an important influence on the diatom assemblages from the epilithon and epiphyton. Epilithon showed the lowest correlation with most of the environmental factors and had significantly lower species diversity than epiphyton, epipelon and epipsammon. Multivariate analysis of the diatom data suggested that in all benthic habitats of the Mesta River seasonal replacement of diatom assemblages was controlled by the water chemistry rather than substratum, current velocity or discharge. The oligotrophic, mesotrophic and eutrophic diatom communities in the Mesta River comprised early-, mid- and late-successional colonizers respectively. Multiple comparisons of all periphytic communities showed that habitat specificity was positively correlated with current velocity.     

Phytoplankton diversity (alpha,beta, and gamma) from the Araguaia River tropical floodplain lakes (central Brazil)

Alpha, beta and gamma are three components of species diversity. Knowing these attributes in floodplain lake phytoplankton communities is vital when selecting conservation areas. Species diversity is commonly used with other taxonomic groups, but rarely with phytoplankton. We compared the number of phytoplankton species (alpha diversity) from 21 Middle Araguaia River floodplain lakes in the 2000 and 2001 rainy and dry seasons. From these samples we estimated complete survey species richness (gamma diversity), quantified differences in species composition between lakes (beta diversity) and assessed the influence of abiotic variables on beta diversity. We recorded a total of 577 taxa. The Sjack1 estimator indicated that 62.31% of taxa were sampled in the 2000 rainy and 67.65% dry seasons, and 68.36% in the 2001 rainy and 73.5% dry seasons. In almost all seasons, alpha diversity negatively correlated with latitude. Beta diversity (β-1) was higher in high water periods, especially in 2000. This may have been caused by isolated heavy rainfall, which would have increased environmental heterogeneity and raised beta diversity. DCA showed differences in phytoplankton composition between rainy and dry seasons in 2000 and 2001, reflecting the influence of flood pulses on phytoplankton composition. The Mantel test indicated spatial distribution patterns where geographically more distant lakes had less-similar phytoplankton communities. Handling editor: J. Padisak     

Subsurface and surface halophile communities of the chaotropic Salar de Uyuni

Salar de Uyuni (SdU) is the biggest athalosaline environment on Earth, holding a high percentage of the known world Li reserves. Due to its hypersalinity, temperature and humidity fluctuations, high exposure to UV radiation, and its elevated concentration of chaotropic agents like MgCl₂, LiCl and NaBr, SdU is considered a polyextreme environment. Here, we report the prokaryotic abundance and diversity of 46 samples obtained in different seasons and geographical areas. The identified bacterial community was found to be more heterogeneous than the archaeal community, with both communities varying geographically. A seasonal difference has been detected for archaea. Salinibacter, Halonotius and Halorubrum were the most abundant genera in Salar de Uyuni. Different unclassified archaea were also detected. In addition, the diversity of two subsurface samples obtained at 20 and 80 m depth was evaluated and compared with the surface data, generating an evolutionary record of a multilayer hypersaline ecosystem.     

Short-term variations in abundances and potential activities of viruses,bacteria and nanoprotists in Lake Bourget

Samples were collected at four depths every 6 h over a 42-h period during two contrasting seasons (June vs. December) from Lake Bourget, France, for evidence of circadian fluctuations in the concentrations and potential activities of viruses, prokaryotes and protists in relation to environmental conditions: temperature, chlorophyll a and dissolved organic carbon (DOC) concentrations. Considerable vertical and temporal fluctuations were observed for all variables. Circadian variations were noted for DOC and chlorophyll a concentrations. Despite the external abiotic forcing (light, water movements), the fluctuations of microbial variables (including viruses) in most cases were apparently linked to biotic factors and interactions. Standing stocks and activities, as well as the number and levels of correlations among the microbial components, were, surprisingly, higher in winter than in summer. We speculate that this was because trophic interactions prevailed over the seasonal forcing (i.e. temperature) in shaping the observed differences.     

Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol

Automated species identification based on data produced with metabarcoding offers an alternative for assessing biodiversity of bulk insect samples obtained with traps. We used a standard two‐step PCR approach to amplify a 313 bp fragment of the barcoding region of the mitochondrial COI gene. The PCR products were sequenced on an Illumina MiSeq platform, and the OTUs production and taxonomic identifications were performed with a customized pipeline and database. The DNA used in the PCR procedures was extracted directly from the preservative ethanol of bulk insect samples obtained with automatic light traps in 12 sampling areas located in different biomes of Brazil, during wet and dry seasons. Agricultural field and forest edge habitats were collected for all sampling areas. A total of 119 insect OTUs and nine additional OTUs assigned to other arthropod taxa were obtained at a ≥97% sequence similarity level. The alpha and beta diversity analyses comparing biomes, habitats, and seasons were mostly inconclusive, except for a significant difference in beta diversity between biomes. In this study, we were able to metabarcode and HTS adult insects from their preservative medium. Notwithstanding, our results underrepresent the true magnitude of insect diversity expected from samples obtained with automatic light traps in Brazil. Although biological and technical factors might have impacted our results, measures to optimize and standardize eDNA HTS should be in place to improve taxonomic coverage of samples of unknown diversity and stored in suboptimal conditions, which is the case of most eDNA samples.     

黏菌物种多样性及其与影响因子关系的研究进展

黏菌是一类具有独特特征且广泛分布在陆地生态系统中的菌物,具有调节微生境微生物群落、影响营养和生物量分配等作用。黏菌的物种多样性及影响因素一直是黏菌生态学的研究热点。本文综述了不同微生境中黏菌的发生情况以及影响黏菌物种多样性的非生物因子和生物因子3个方面的研究进展,进一步揭示黏菌在生态系统中的生态功能。     

Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods

There is a paucity of knowledge on microbial community diversity and naturally occurring seasonal variations in agricultural soil. For this purpose the soil microbial community of a wheat field on an experimental farm in The Netherlands was studied by using both cultivation-based and molecule-based methods. Samples were taken in the different seasons over a 1-year period. Fatty acid-based typing of bacterial isolates obtained via plating revealed a diverse community of mainly gram-positive bacteria, and only a few isolates appeared to belong to the Proteobacteria and green sulfur bacteria. Some genera, such as Micrococcus, Arthrobacter, and Corynebacterium were detected throughout the year, while Bacillus was found only in July. Isolate diversity was lowest in July, and the most abundant species, Arthrobacter oxydans, and members of the genus Pseudomonas were found in reduced numbers in July. Analysis by molecular techniques showed that diversity of cloned 16S ribosomal DNA (rDNA) sequences was greater than the diversity among cultured isolates. Moreover, based on analysis of 16S rDNA sequences, there was a more even distribution among five main divisions, Acidobacterium, Proteobacteria, Nitrospira, cyanobacteria, and green sulfur bacteria. No clones were found belonging to the gram-positive bacteria, which dominated the cultured isolates. Seasonal fluctuations were assessed by denaturing gradient gel electrophoresis. Statistical analysis of the banding patterns revealed significant differences between samples taken in different seasons. Cluster analysis of the patterns revealed that the bacterial community in July clearly differed from those in the other months. Although the molecule- and cultivation-based methods allowed the detection of different parts of the bacterial community, results from both methods indicated that the community present in July showed the largest difference from the communities of the other months. Efforts were made to use the sequence data for providing insight into more general ecological relationships. Based on the distribution of 16S rDNA sequences among the bacterial divisions found in this work and in literature, it is suggested that the ratio between the number of Proteobacteria and Acidobacterium organisms might be indicative of the trophic level of the soil.     

Seasonal Distribution and Diversity of Ground Arthropods in Microhabitats Following a Shrub Plantation Age Sequence in Desertified Steppe

In desertified regions, shrub-dominated patches are important microhabitats for ground arthropod assemblages. As shrub age increases, soil, vegetation and microbiological properties can change remarkably and spontaneously across seasons. However, relatively few studies have analyzed how ground arthropods respond to the microhabitats created by shrubs of different plantation ages across seasons. Using 6, 15, 24 and 36 year-old plantations of re-vegetated shrubs (Caragana koushinskii) in the desert steppe of northwestern China as a model system, we sampled ground arthropod communities using a pitfall trapping method in the microhabitats under shrubs and in the open areas between shrubs, during the spring, summer and autumn. The total ground arthropod assemblage was dominated by Carabidae, Melolonthidae, Curculionidae, Tenebrionidae and Formicidae that were affected by plantation age, seasonal changes, or the interaction between these factors, with the later two groups also influenced by microhabitat. Overall, a facilitative effect was observed, with more arthropods and a greater diversity found under shrubs as compared to open areas, but this was markedly affected by seasonal changes. There was a high degree of similarity in arthropod assemblages and diversity between microhabitats in summer and autumn. Shrub plantation age significantly influenced the distribution of the most abundant groups, and also the diversity indices of the ground arthropods. However, there was not an overall positive relationship between shrub age and arthropod abundance, richness or diversity index. The influence of plantation age on arthropod communities was also affected by seasonal changes. From spring through summer to autumn, community indices of ground arthropods tended to decline, and a high degree of similarity in these indices (with fluctuation) was observed among different ages of shrub plantation in autumn. Altogether the recovery of arthropod communities was markedly affected by seasonal variability, and they demonstrated distinctive communal fingerprints in different microhabitats for each plantation age stage.     

Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula,Mexico

Aim

Desert springs or oases are the only permanent mesic environments in highly water-limited arid regions. Oases have immense cultural, evolutionary and ecological importance for people and a high number of endemic and relic species. Nevertheless, they are also highly vulnerable ecosystems, with invasive species, overexploitation and climate change being the primary threats. We used the arthropod communities' spatiotemporal diversity and distribution patterns as a proxy to understand biodiversity dynamics in two geographically close but ecologically contrasting and highly threatened ecosystems: deserts and oases.

Location

Baja California Peninsula, Mexico.

Methods

Arthropod communities at five oases and surrounding desert scrub areas were sampled in two seasons. Using DNA metabarcoding and traditional taxonomic surveys, we tried to identify what biotic and abiotic characteristics of the habitat are important drivers of arthropod diversity and how these characteristics can change across spatial and temporal scales.

Results

Over 6200 individuals representing 23 orders were collected. In oasis samples, the community composition fluctuated more in space (i.e. among sites) than in time (i.e. seasons). Thus, seasonal changes did not affect oasis community diversity and composition, but the dissimilarity among sites increased with geographic distance. Moreover, anthropic activities negatively correlated with arthropod diversity in oases. On the other hand, the season, geography (e.g. latitude) and biotic characteristics of the habitat (e.g. sampled scrub species) significantly affected the diversity and composition of the desert arthropod communities.

Main Conclusions

Neutral dynamics (e.g. historical climatic events, dispersal limitation and spatial component) and human impact significantly influenced the biodiversity patterns of each oasis. In contrast, the habitat's seasonal variation and biotic characteristics were the most important variables influencing the diversity of the desert communities. Baja California oases harbour distinct invertebrate communities; therefore, each oasis should be conserved individually to preserve these unique assemblages.     

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

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