Response of marine communities to local temperature changes

As global climate change and variability drive shifts in species’ distributions, ecological communities are being reorganized. One approach to understand community change in response to climate change has been to characterize communities by a collective thermal preference, or community temperature index (CTI), and then to compare changes in CTI with changes in temperature. However, important questions remain about whether and how responsive communities are to changes in their local thermal environments. We used CTI to analyze changes in 160 marine assemblages (fish and invertebrates) across the rapidly‐changing Northeast U.S. Continental Shelf Large Marine Ecosystem and calculated expected community change based on historical relationships between species presence and temperature from a separate training dataset. We then compared interannual and long‐term temperature changes with expected community responses and observed community responses over both temporal scales. For these marine communities, we found that community composition as well as composition changes through time could be explained by species associations with bottom temperature. Individual species had non‐linear responses to changes in temperature, and these nonlinearities scaled up to a nonlinear relationship between CTI and temperature. On average, CTI increased by 0.36°C (95% CI: 0.34–0.38°C) for every 1°C increase in bottom temperature, but the relationship between CTI and temperature also depended on community composition. In addition, communities responded more strongly to interannual variation than to long‐term trends in temperature. We recommend that future research into climate‐driven community change accounts for nonlinear responses and examines ecological responses across a range of temporal and geographical scales.     

Relationship of seed source and arbuscular mycorrhizal fungi inoculum type to growth and colonization of big bluestem (Andropogon gerardii)

Big bluestem (Andropogon gerardii) is a key grass of tallgrass prairies and is commonly included in restoration projects. In many cases, it has been found to benefit significantly from arbuscular mycorrhizal (AM) fungi, however results have varied under non-sterile soil conditions. This study investigated the effects of two types of AM fungi inoculum (commercial and prairie) on growth and root colonization of big bluestem from five different seed sources grown in non-sterile soils. Seed sources were collected from five remnant prairies in the Tallgrass Prairie Peninsula located in the Midwestern United States. Growth of big bluestem and root length colonized by AM fungi was highly variable among seed source treatments. Overall, percentage of root length colonized by AM fungi was positively correlated with the total dry weight of plants, and plants that received inoculum generally grew better than those that did not receive inoculum. Inoculum treatment affected both big bluestem growth and percentage root length colonized and there was an interaction between seed source and inoculum treatment relative to colonization. Root colonization responses were not significantly different between the prairie and commercial inoculum types, although there was a significant response between plants that received additional inoculum as opposed to no additional inoculum. Seed sources from Ohio and Illinois had the highest biomasses and greatest percentage of root length colonized while plants from Wisconsin and Missouri grew poorly and had low root colonization. These results demonstrate the importance of considering both seed source and inoculum type before the incorporation of AM inoculum to prairie restoration projects.     

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees

Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.     

Disentangling environmental and host sources of fungal endophyte communities in an experimental beachgrass study

Disentangling the ecological factors that contribute to the assembly of the microbial symbiont communities within eukaryotic hosts is an ongoing challenge. Broadly speaking, symbiont propagules arrive either from external sources in the environment or from internal sources within the same host individual. To understand the relative importance of these propagule sources to symbiont community assembly, we characterized symbiotic fungal endophyte communities within the roots of three species of beachgrass in a field experiment. We manipulated two aspects of the external environment, successional habitat and physical disturbance. To determine the role of internal sources of propagules for endophyte community assembly, we used beachgrass individuals with different pre‐existing endophyte communities. Endophyte species richness and community composition were characterized using culture‐based and next‐generation sequencing approaches. Our results showed that external propagule sources associated with successional habitat, but not disturbance, were particularly important for colonization of most endophytic taxa. In contrast, internal propagule sources played a minor role for most endophytic taxa but were important for colonization by the dominant taxon Microdochium bolleyi. Our findings highlight the power of manipulative field experiments to link symbiont community assembly to its underlying ecological processes, and to ultimately improve predictions of symbiont community assembly across environments.     

Effects of host plant environment and Ustilago maydis infection on the fungal endophyte community of maize (Zea mays)

The focus of many fungal endophyte studies has been how plants benefit from endophyte infection. Few studies have investigated the role of the host plant as an environment in shaping endophyte community diversity and composition. The effects that different attributes of the host plant, that is, host genetic variation, host variation in resistance to the fungal pathogen Ustilago maydis and U. maydis infection, have on the fungal endophyte communities in maize (Zea mays) was examined. The internal transcribed spacer (ITS) region of the rDNA was sequenced to identify fungi and the endophyte communities were compared in six maize lines that varied in their resistance to U. maydis. It was found that host genetic variation, as determined by maize line, had significant effects on species richness, while the interactions between line and U. maydis infection and line and field plot had significant effects on endophyte community composition. However, the effects of maize line were not dependent on whether lines were resistant or susceptible to U. maydis. Almost 3000 clones obtained from 58 plants were sequenced to characterize the maize endophyte community. These results suggest that the endophyte community is shaped by complex interactions and factors, such as inoculum pool and microclimate, may be important.     

Molecular approach to the characterisation of fungal communities: methods for DNA extraction, PCR amplification and DGGE analysis of painted art objects

A protocol for efficient extraction of fungal DNA from micromycetes colonising painted art objects was developed. Polymerase chain reaction (PCR) inhibitors were successfully removed by a combined application of a Chelex-100 adsorption resin and a Geneclean Kit for Ancient DNA. Universal fungal primers for PCR amplification of 28S rDNA (U1 and U2) were tested for their applicability in denaturing gradient gel electrophoresis (DGGE) analysis of fungal communities. Artificially produced mortar samples inoculated with fungal pure cultures isolated from mural paintings were used as model objects for DNA extractions and DGGE analysis. Good resolution in DGGE was achieved using 260-bp rDNA fragments amplified with U1/DGGE and U2 primers directly from model communities.     

半干旱黄土区不同管理措施下草地群落结构对短期氮、水添加的响应

氮沉降和降水变异显著影响草地群落结构和功能,但缺乏对不同管理措施下草地群落结构对氮沉降和降水变异响应的研究。为模拟不同管理措施下草地群落结构对氮沉降和降水变异的响应特征,以半干旱黄土区云雾山国家自然保护区典型草原为研究对象,系统分析了在封育、刈割和火烧三种管理措施下,氮添加和水添加对群落地上生物量、功能群组成和群落多样性的影响。结果表明,氮添加和水添加对地上生物量、功能群组成和群落多样性指数的影响因管理措施不同有所差异。（1）在封育草地上,氮添加显著降低物种多样性,对地上生物量影响较小;水添加显著增加物种多样性指数,氮添加和水添加的交互作用显著增加地上生物量、禾本科所占比例和莎草科所占比例;物种多样性指数均与地上生物量无显著相关,与不同功能群所占比例显著相关。（2）在刈割草地上,氮添加和水添加显著提高草地群落地上生物量,氮添加和水添加交互作用尤为显著;氮添加和水添加显著增加物种丰富度指数,对物种均匀度影响较小;杂草类所占比例和地上生物量对Shannon-Weiner多样性指数的贡献率较大。（3）在火烧草地上,氮添加和水添加显著提高群落地上生物量,对物种多样性的影响因年份不同有所差异,氮添加和水添加交互作用具有累加效应;Shannon-Weiner多样性指数与地上生物量呈显著负相关,与莎草科所占比例呈显著正相关。研究表明管理措施显著影响群落结构对氮添加和水添加的响应特征,亦改变生产力和物种多样性的关系模式,为更好地应对全球变化进行草地管理提供数据支撑。     

Site‐specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales

The plant microbiome can affect host function in many ways and characterizing the ecological factors that shape endophytic (microbes living inside host plant tissues) community diversity is a key step in understanding the impacts of environmental change on these communities. Phylogenetic relatedness among members of a community offers a way of quantifying phylogenetic diversity of a community and can provide insight into the ecological factors that shape endophyte microbiomes. We examined the effects of experimental nutrient addition and herbivory exclusion on the phylogenetic diversity of foliar fungal endophyte communities of the grass species Andropogon gerardii at four sites in the Great Plains of the central USA. Using amplicon sequencing, we characterized the effects of fertilization and herbivory on fungal community phylogenetic diversity at spatial scales that spanned within‐host to between sites across the Great Plains. Despite increasing fungal diversity and richness, at larger spatial scales, fungal microbiomes were composed of taxa showing random phylogenetic associations. Phylogenetic diversity did not differ systematically when summed across increasing spatial scales from a few meters within plots to hundreds of kilometers among sites. We observed substantial shifts in composition across sites, demonstrating distinct but similarly diverse fungal communities were maintained within sites across the region. In contrast, at the scale of within leaves, fungal communities tended to be comprised of closely related taxa regardless of the environment, but there were no shifts in phylogenetic composition among communities. We also found that nutrient addition (fertilization) and herbivory have varying effects at different sites. These results suggest that the direction and magnitude of the outcomes of environmental modifications likely depend on the spatial scale considered, and can also be constrained by regional site differences in microbial diversity and composition.     

荒漠草原植物群落结构及其稳定性对增水和增氮的响应

通过在荒漠草原开展增水和增氮野外控制试验,研究增水和增氮对荒漠草原植物群落结构、物种多样性及群落稳定性的影响。结果表明：（1）增水和增氮处理显著影响了荒漠草原植物群落结构和地上生物量,而对植物群落稳定性影响不显著（P>0.05）。增水处理显著增加了豆科和禾本科植物地上生物量（101.3%和57.9%）（P<0.05）;增水+增氮处理显著增加了植物群落盖度（43.2%）和地上生物量（112.4%）及不同功能群（禾本科和杂类草）植物盖度（75.5%和47.3%）和地上生物量（139.3%和85.7%）（P<0.05）。与增氮处理相比,增水+增氮处理显著增加了植物群落和不同功能群（禾本科和杂类草）植物高度、盖度和地上生物量（P<0.05）。（2）增水、增氮和增水+增氮处理均显著降低了植物群落Pielou指数（11.7%、8.7%和10.2%）（P<0.05）。（3）增水和增水+增氮处理提高了荒漠草原植物群落稳定性,而增氮处理降低了荒漠草原植物群落稳定性。增水处理荒漠草原植物群落稳定性效应大于增水+增氮处理。研究表明,荒漠草原植物群落结构受到氮沉降和降水增加的共同影响。增加降水对荒漠草原植物群落稳定性的积极效应可能会抵消部分氮沉降的消极影响,荒漠草原植物群落地上生物量及群落稳定性可能有所增加。     

Environmental factors and host genetic variation shape the fungal endophyte communities within needles of Scots pine (Pinus sylvestris)

To determine the role of environmental and host genetic factors in shaping fungal endophyte communities we used culturing and metabarcoding techniques to quantify fungal taxa within healthy Scots pine (Pinus sylvestris) needles in a 7-y old provenance-progeny trial replicated at three sites. Both methods revealed a community of ascomycete and basidiomycete taxa dominated by the needle pathogen Lophodermium seditiosum. Differences in fungal endophyte taxon composition and diversity indices were highly significant among trial sites. Within two sites, fungal endophyte communities varied significantly among provenances. Furthermore, the communities differed significantly among maternal families within provenances in 11/15 and 7/15 comparisons involving culture and metabarcoding data respectively. We conclude that both environmental and host genetic variation shape the fungal endophyte community of P. sylvestris needles.     

芨芨草叶片养分特征对氮磷不同添加水平的响应

植物叶片氮(N)、磷(P)养分特征受土壤可利用性N、P含量和N、P相对比例(N:P)的共同影响, 研究其作用机制有助于解释和评估土壤养分变化对植物养分利用策略的影响。该研究通过盆栽实验, 探讨芨芨草(Achnatherum splendens)养分化学计量学特征和叶片养分回收特征对不同剂量的养分添加(低、中、高3个N添加水平: 1.5、4.5、13.5 g·m^-2·a^-1)及不同土壤N:P (5、15、25)的响应。结果表明: 养分添加水平的提高显著增加了成熟叶片P含量和衰老叶片N、P含量, 显著降低了叶片N、P养分回收效率(NRE, PRE)。土壤N:P的升高显著降低了衰老叶片P含量和叶片NRE, 但增加了成熟和衰老叶片N:P和叶片PRE。相同养分添加水平条件下, 土壤N:P与叶片PRE显著正相关, 但与叶片NRE无显著相关性; 相同N:P条件下, 养分添加水平与NRE负相关, 但与PRE无显著相关性。植物NRE:PRE可以有效地反映环境变化所导致的植物对N、P需求的改变。土壤养分添加水平和N:P共同影响着芨芨草的叶片养分生态化学计量学特征和养分回收。     

Cultivar-level genotype differences influence diversity and composition of lettuce (Lactuca sp.) phyllosphere fungal communities

Different lettuce genotypes supported significantly different phyllosphere fungal communities. Phyllosphere fungal diversity was low and fungi fell into five similarity groups. These groups were represented in significantly different proportions throughout 26 lettuce accessions indicating cultivar-level variation in the fungal colonization of the lettuce phyllosphere. Significant differences in the proportions of the two dominant groups (with similarity to Cladosporium spp. and Sporobolomyces roseus) were identified between parental lines of two lettuce mapping populations providing opportunities to further investigate the genetic control of cultivar-level variation in fungal phyllosphere colonisation.     

More than one way to be an herbivore: convergent evolution of herbivory using different digestive strategies in prickleback fishes (Stichaeidae)

In fishes, the evolution of herbivory has occured within a spectrum of digestive strategies, with two extremes on opposite ends: (i) a rate-maximization strategy characterized by high intake, rapid throughput of food through the gut, and little reliance on microbial digestion or (ii) a yield-maximization strategy characterized by measured intake, slower transit of food through the gut, and more of a reliance on microbial digestion in the hindgut. One of these strategies tends to be favored within a given clade of fishes. Here, we tested the hypothesis that rate or yield digestive strategies can arise in convergently evolved herbivores within a given lineage. In the family Stichaeidae, convergent evolution of herbivory occured in Cebidichthys violaceus and Xiphister mucosus, and despite nearly identical diets, these two species have different digestive physiologies. We found that C. violaceus has more digesta in its distal intestine than other gut regions, has comparatively high concentrations (>11 mM) of short-chain fatty acids (SCFA, the endpoints of microbial fermentation) in its distal intestine, and a spike in β-glucosidase activity in this gut region, findings that, when coupled to long retention times (>20 h) of food in the guts of C. violaceus, suggest a yield-maximizing strategy in this species. X. mucosus showed none of these features and was more similar to its sister taxon, the omnivorous Xiphister atropurpureus, in terms of digestive enzyme activities, gut content partitioning, and concentrations of SCFA in their distal intestines. We also contrasted these herbivores and omnivores with other sympatric stichaeid fishes, Phytichthys chirus (omnivore) and Anoplarchus purpurescens (carnivore), each of which had digestive physiologies consistent with the consumption of animal material. This study shows that rate- and yield-maximizing strategies can evolve in closely related fishes and suggests that resource partitioning can play out on the level of digestive physiology in sympatric, closely related herbivores.     

The presence of aggressive ants is associated with fewer insect visits to and altered microbe communities in coffee flowers

The process of dispersal can shape ecological communities, but its influence is thought to be small compared to the effects of environmental variation or direct species interactions, particularly for microbial communities. Ants can influence movement patterns of insects and the microbes they vector, potentially affecting microbial establishment on plants, including in agroecosystems. Here, we examine how the presence of aggressive ants, which can influence floral visitation by bees and other pollinators, shapes the community composition of bacteria and fungi on coffee flowers in farms that differ in shade management intensity. We hypothesized that the presence of aggressive ants should reduce the frequency and diversity of floral visitors. Finally, we predicted that the effects of ants should be stronger in the low-shade farm, which has a less diverse community of floral visitors. We sampled microbial communities from nectar and pistils of coffee flowers near and far from nests of the aggressive ant Azteca sericeasur across two farms that vary in shade management and diversity of floral visitors. Bacterial and fungal community composition was characterized using Illumina sequencing of the 16S and ITS regions of the rRNA gene. Consistent with our expectation, Azteca presence was associated with a decrease in the number and diversity of visitors, visit duration and number of flowers visited. Azteca presence influenced microbial communities, but effects differed between farms. Azteca nests were associated with higher bacterial diversity in both farms, but the difference between flowers on trees with and without Azteca was greater in the high-shade farm. Azteca nests were associated with higher fungal diversity in the high-shade farm, but not the low-shade farm. In addition, the presence of ants was strongly associated with species composition of fungi and bacteria in flowers, but differentiation between ant and no-ant communities was greater in the low-shade farm. Specific operational taxonomic units (OTUs) were differentially associated with the presence of ants. We conclude that indirect interactions that influence dispersal may have large effects on microbial community composition, particularly in ephemeral microbial communities.     

Linking wood-decay fungal communities to decay rates: Using a long-term experimental manipulation of deadwood and canopy gaps

Decomposition transfers carbon (C) from detrital organic matter to soil and atmospheric pools. In forested ecosystems, deadwood accounts for a large proportion of the detrital C pool and is primarily decomposed by wood-inhabiting fungi (WIF). Deadwood reductions linked to forest harvesting may alter WIF richness and composition, thus indirectly influencing the persistence of deadwood and its contribution to C and nutrient cycling. Forest structure was enhanced via canopy gap creation and coarse woody debris (CWD) addition that mimic natural disturbance by windfall within a deciduous northern hardwood forest (Wisconsin, USA) to examine its effect on deadwood-associated biodiversity and function. Experimental sugar maple (Acer saccharum) logs were sampled, for DNA extraction, ten years after placement to determine the assembly of fungal community composition and its relationship to wood decay rates.Our findings suggest that the WIF community responded to gap disturbance by favoring species able to persist under more extreme microclimates caused by gaps. CWD addition under closed canopy tended to favor a different species assemblage from gap creation treatments and the control, where canopy was undisturbed and CWD was not added. This was presumably due to consistent microclimatic conditions and the abundance of CWD substrates for host specialists. Fungal OTU richness was significantly and inversely related to CWD decay rates, likely due to competition for resources. In contrast, fungal OTU composition was not significantly related to CWD decay rates, canopy openness or CWD addition amounts. Our study site represents a diverse fungal community in which complex interactions among wood-inhabiting organisms and abiotic factors are likely to slow CWD decomposition, which suggests that maintaining a biodiverse and microsite-rich ecosystem may enhance the capacity for C storage within temperate forests.     

Response of compost maturity and microbial community composition to pentachlorophenol (PCP)-contaminated soil during composting

Two composting piles were prepared by adding to a mixture of rice straw, vegetables and bran: (i) raw soil free from pentachlorophenol (PCP) contamination (pile A) and (ii) PCP-contaminated soil (pile B). It was shown by the results that compost maturity characterized by water soluble carbon (WSC), TOC/TN ratio, germination index (GI) and dehydrogenase activity (DA) was significantly affected by PCP exposure, which resulted in an inferior degree of maturity for pile B. DGGE analysis revealed an inhibited effect of PCP on compost microbial abundance. The bacteria community shifts were mainly consistent with composting factors such as temperature, pH, moisture content and substrates. By contrast, the fungal communities were more sensitive to PCP contamination due to the significant correlation between fungal community shifts and PCP removal. Therefore, the different microbial community compositions for properly evaluating the degree of maturity and PCP contamination were suggested.     

Trait dynamics of Mediterranean xerophytic shrub communities growing on stabilised inland dunes respond to nutrient and aridity gradients

Background: Understanding the processes that determine community assembly and their dynamics is a central issue in ecology. The analysis of functional diversity can improve our understanding of these dynamics by identifying community assembly processes.

Aims: We studied the effect of environment–community covariations on both functional diversity and functional structure of xerophytic shrub communities for inferring the community assembly processes shaping this vegetation type.

Methods: Functional diversity was quantified using (1) community-weighted mean of the studied traits, (2) functional groups, defined using Ward’s hierarchical agglomerative clustering method and (3) Rao’s quadratic entropy. Relationships between functional diversity and environmental gradients were identified by Spearman correlations and modelled using generalised additive models.

Results: Variations in community composition and functional diversity correlated with soil nutrient availability and aridity. Increasing nutrient availability resulted in both greater average plant height and higher abundance of plants with green photosynthetic organ colour, whereas the abundance of nanophanerophytes increases with aridity.

Conclusions: The species composition and trait structure of the studied Mediterranean xerophytic shrub communities varies along nutrient and aridity gradients. This supports the importance of environmental filters for the local assembly and dynamics of these inland dune communities.     

Inventory,diversity and communities of macrofungi in the Collestrada forest (Umbria,central Italy)

In this study, an inventory of the macrofungi in the Collestrada forest (Umbria, Italy).was performed through the collection of sporocarps of basidiomycetes and ascomycetes over a period of three years. Sampling was performed in selected sites’ representatives of the seven wood types present in the Collestrada forest. A total of 341 species were identified and a comprehensive spatial and seasonal analysis of macrofungal species richness, abundance and diversity was performed. Patterns of fungal fructification varied greatly between species and ecological groups, over the years and seasons. Differences in fungal species composition and abundance were detected between the wood types, however, changes of meteorogical conditions, especially the rainfall level and relative humidity, during the growing seasons and years have a major impact on determining the structure of fungal communities. As 143 of the fungal species identified matched with those included in the Red List (or proposals for Red Lists) in several European countries, the studied sites may represent important areas for conservation of fungal diversity (IFA). The results of this study constitute a powerful tool to optimize conservation strategies and policy.