Fire-modulated fluctuations in nutrient availability stimulate biome-scale floristic turnover in time, and elevated species richness, in low-nutrient fynbos heathland

BACKGROUND AND AIMS

In many systems, postfire vegetation recovery is characterized by temporal changes in plant species composition and richness. We attribute this to changes in resource availability with time since fire, with the magnitude of species turnover determined by the degree of resource limitation. Here, we test the hypothesis that postfire species turnover in South African fynbos heathland is powered by fire-modulated changes in nutrient availability, with the magnitude of turnover in nutrient-constrained fynbos being greater than in fertile renosterveld shrubland. We also test the hypothesis that floristic overlaps between fynbos and renosterveld are attributable to nutritional augmentation of fynbos soils immediately after fire.

METHODS

We use vegetation survey data from two sites on the Cape Peninsula to compare changes in species richness and composition with time since fire.

KEY RESULTS

Fynbos communities display a clear decline in species richness with time since fire, whereas no such decline is apparent in renosterveld. In fynbos, declining species richness is associated with declines in the richness of plant families having high foliar concentrations of nitrogen, phosphorus and potassium and possessing attributes that are nutritionally costly. In contrast, families that dominate late-succession fynbos possess adaptations for the acquisition and retention of sparse nutrients. At the family level, recently burnt fynbos is compositionally more similar to renosterveld than is mature fynbos.

CONCLUSIONS

Our data suggest that nutritionally driven species turnover contributes significantly to fynbos community richness. We propose that the extremely low baseline fertility of fynbos soils serves to lengthen the nutritional resource axis along which species can differentiate and coexist, thereby providing the opportunity for low-nutrient extremophiles to coexist spatially with species adapted to more fertile soil. This mechanism has the potential to operate in any resource-constrained system in which episodic disturbance affects resource availability.

Temporal Dynamics and Contribution of Phage Community to the Prevalence of Antibiotic Resistance Genes in a Full-Scale Sludge Anaerobic Digestion Plant

Anaerobic digestion (AD) is an important biological resource recovery process, where microorganisms play key roles for material transformation. There has been some knowledge about the prokaryotic community and antibiotic resistance genes (ARGs) in AD, but there has been very limited knowledge of phages. In this study, samples from a full-scale AD plant were collected over 13 months, sequenced, and analyzed for viral and prokaryotic metagenomes. Totally, 3015 viral operational taxonomic units (vOTUs) were detected, mostly assigned to Caudoviricetes. The phage community had faster temporal variation than the prokaryotic community. Warm seasons harbored a higher abundance of both temperate phages and broad host-range phages. Seven ARGs of 6 subtypes were carried by 20 vOTUs, a representative ermT gene was synthesized and expressed, and the resistance activity in the host was examined, confirming the real activity of virus-carried ARGs in the AD process. Some of the ARGs were horizontally transferred between the phage and prokaryotic genomes. However, phage infection was not found to contribute to ARG transfer. This study provided an insight into the ecological patterns of the phage community, confirmed the antibiotic resistance activity of virus-carried ARGs, evaluated the contribution of phages on the ARG prevalence, and laid the foundation for the control strategies of the community and antibiotic resistance in the AD process.

Stable coexistence or competitive exclusion? Fern endophytes demonstrate rapid turnover favouring a dominant fungus

Fungal endophytes are critical members of the plant microbiome, but their community dynamics throughout an entire growing season are underexplored. Additionally, most fungal endophyte research has centred on seed-reproducing hosts, while spore-reproducing plants also host endophytes and may be colonized by unique community members. In order to examine annual fungal endophyte community dynamics in a spore-reproducing host, we explored endophytes in a single population of ferns, Polystichum munitum, in the Pacific Northwest. Through metabarcoding, we characterized the community assembly and temporal turnover of foliar endophytes throughout a growing season. From these results, we selected endophytes with outsized representations in sequence data and performed in vitro competition assays. Finally, we inoculated sterile fern gametophytes with dominant fungi observed in the field and determined their effects on host performance. Sequencing demonstrated that ferns were colonized by a diverse community of fungal endophytes in newly emerged tissue, but diversity decreased throughout the season leading to the preponderance of a single fungus in later sampling months. This previously undescribed endophyte appears to abundantly colonize the host to the detriment of other microfungi. Competition assays on a variety of media types failed to demonstrate that the dominant fungus was competitive against other fungi isolated from the same hosts, and inoculation onto sterile fern gametophytes did not alter growth compared to sterile controls, suggesting its effects are not antagonistic. The presence of this endophyte in the fern population probably demonstrates a case of repeated colonization driving competitive exclusion of other fungal community members.

Rapid bacterial and fungal successional dynamics in first year after chaparral wildfire

The rise in wildfire frequency and severity across the globe has increased interest in secondary succession. However, despite the role of soil microbial communities in controlling biogeochemical cycling and their role in the regeneration of post-fire vegetation, the lack of measurements immediately post-fire and at high temporal resolution has limited understanding of microbial secondary succession. To fill this knowledge gap, we sampled soils at 17, 25, 34, 67, 95, 131, 187, 286, and 376 days after a southern California wildfire in fire-adapted chaparral shrublands. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition with Illumina MiSeq sequencing of 16S and ITS2 amplicons. Fire severely reduced bacterial biomass by 47%, bacterial richness by 46%, fungal biomass by 86%, and fungal richness by 68%. The burned bacterial and fungal communities experienced rapid succession, with 5-6 compositional turnover periods. Analogous to plants, turnover was driven by "fire-loving" pyrophilous microbes, many of which have been previously found in forests worldwide and changed markedly in abundance over time. Fungal secondary succession was initiated by the Basidiomycete yeast Geminibasidium, which traded off against the filamentous Ascomycetes Pyronema, Aspergillus, and Penicillium. For bacteria, the Proteobacteria Massilia dominated all year, but the Firmicute Bacillus and Proteobacteria Noviherbaspirillum increased in abundance over time. Our high-resolution temporal sampling allowed us to capture post-fire microbial secondary successional dynamics and suggest that putative tradeoffs in thermotolerance, colonization, and competition among dominant pyrophilous microbes control microbial succession with possible implications for ecosystem function.

Temporal turnover of the soil microbiome composition is guild-specific

Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.

Temporal turnover in mycorrhizal interactions: a proof of concept with orchids

Temporal turnover events in biotic interactions involving plants are rarely assessed, although such changes might afford a considerable acclimation potential to the plant. This could enable fairly rapid responses to short-term fluctuations in growth conditions as well as lasting responses to long-term climatic trends. Here, we present a classification of temporal turnover encompassing 11 possible scenarios. Using orchid mycorrhiza as a study model, we show that temporal changes are common, and discuss under which conditions temporal turnover of fungal symbiont is expected. We provide six research questions and identify technical challenges that we deem most important for future studies. Finally, we discuss how the same framework can be applied to other types of biotic interactions.

Diurnal Temperature Variation and Plants Drive Latitudinal Patterns in Seasonal Dynamics of Soil Microbial Community

Seasonality, an exogenous driver, motivates the biological and ecological temporal dynamics of animal and plant communities. Underexplored microbial temporal endogenous dynamics hinders the prediction of microbial response to climate change. To elucidate temporal dynamics of microbial communities, temporal turnover rates, phylogenetic relatedness, and species interactions were integrated to compare those of a series of forest ecosystems along latitudinal gradients. The seasonal turnover rhythm of microbial communities, estimated by the slope (w value) of similarity-time decay relationship, was spatially structured across the latitudinal gradient, which may be caused by a mixture of both diurnal temperature variation and seasonal patterns of plants. Statistical analyses revealed that diurnal temperature variation instead of average temperature imposed a positive and considerable effect alone and also jointly with plants. Due to higher diurnal temperature variation with more climatic niches, microbial communities might evolutionarily adapt into more dispersed phylogenetic assembly based on the standardized effect size of MNTD metric, and ecologically form higher community resistance and resiliency with stronger network interactions among species. Archaea and the bacterial groups of Chloroflexi, Alphaproteobacteria, and Deltaproteobacteria were sensitive to diurnal temperature variation with greater turnover rates at higher latitudes, indicating that greater diurnal temperature fluctuation imposes stronger selective pressure on thermal specialists, because bacteria and archaea, single-celled organisms, have extreme short generation period compared to animal and plant. Our findings thus illustrate that the dynamics of microbial community and species interactions are crucial to assess ecosystem stability to climate variations in an increased climatic variability era.

Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilisation

Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major forms of environmental change - fertilisation and herbivore loss - are affected by species pool size and spatial compositional heterogeneity. Fertilisation led to higher rates of local extinction, whereas turnover in herbivore exclusion plots was driven by species replacement. Overall, sites with more spatially heterogeneous composition showed significantly higher rates of annual turnover, independent of species pool size and treatment. Taking into account spatial biodiversity aspects will therefore improve our understanding of consequences of global and anthropogenic change on community dynamics.

The prevalence and impact of transient species in ecological communities

Transient species occur infrequently in a community over time and do not maintain viable local populations. Because transient species interact differently than non-transients with their biotic and abiotic environment, it is important to characterize the prevalence of these species and how they impact our understanding of ecological systems. We quantified the prevalence and impact of transient species in communities using data on over 19,000 community time series spanning an array of ecosystems, taxonomic groups, and spatial scales. We found that transient species are a general feature of communities regardless of taxa or ecosystem. The proportion of these species decreases with increasing spatial scale leading to a need to control for scale in comparative work. Removing transient species from analyses influences the form of a suite of commonly studied ecological patterns including species-abundance distributions, species-energy relationships, species-area relationships, and temporal turnover. Careful consideration should be given to whether transient species are included in analyses depending on the theoretical and practical relevance of these species for the question being studied.

Divergent biodiversity change within ecosystems

The Earth's ecosystems are under unprecedented pressure, yet the nature of contemporary biodiversity change is not well understood. Growing evidence that community size is regulated highlights the need for improved understanding of community dynamics. As stability in community size could be underpinned by marked temporal turnover, a key question is the extent to which changes in both biodiversity dimensions (temporal α- and temporal β-diversity) covary within and among the assemblages that comprise natural communities. Here, we draw on a multiassemblage dataset (encompassing vertebrates, invertebrates, and unicellular plants) from a tropical freshwater ecosystem and employ a cyclic shift randomization to assess whether any directional change in temporal α-diversity and temporal β-diversity exceeds baseline levels. In the majority of cases, α-diversity remains stable over the 5-y time frame of our analysis, with little evidence for systematic change at the community level. In contrast, temporal β-diversity changes are more prevalent, and the two diversity dimensions are decoupled at both the within- and among-assemblage level. Consequently, a pressing research challenge is to establish how turnover supports regulation and when elevated temporal β-diversity jeopardizes community integrity.

Discordant Temporal Turnovers of Sediment Bacterial and Eukaryotic Communities in Response to Dredging: Nonresilience and Functional Changes

To study the stability and succession of sediment microbial and macrobenthic communities in response to anthropogenic disturbance, a time-series sampling was conducted before, during, and 1 year after dredging in the Guan River in Changzhou, China, which was performed with cutter suction dredgers from 10 April to 20 May 2014. The microbial communities were analyzed by sequencing bacterial 16S rRNA and eukaryotic 18S rRNA gene amplicons with Illumina MiSeq, and the macrobenthic community was identified using a morphological approach simultaneously. The results indicated that dredging disturbance significantly altered the composition and structures of sediment communities. The succession rates of communities were estimated by comparing the slopes of time-decay relationships. The temporal turnover of microeukaryotes (w = 0.3251, P < 0.001 [where w is a measure of the rate of log(species turnover) across log(time)]) was the highest, followed by that of bacteria (w = 0.2450, P < 0.001), and then macrobenthos (w = 0.1273, P < 0.001). During dredging, the alpha diversities of both bacterial and microeukaryotic communities were more resistant, but their beta diversities were less resistant than that of macrobenthos. After recovery for 1 year, all three sediment communities were not resilient and had reached an alternative state. The alterations in sediment community structure and stability resulted in functional changes in nitrogen and carbon cycling in sediments. Sediment pH, dissolved oxygen, redox potential, and temperature were the most important factors influencing the stability of sediment communities and ecosystem multifunctionality. This study suggests that discordant temporal turnovers and nonresilience of sediment communities under dredging resulted in functional changes, which are important for predicting sediment ecosystem functions under anthropogenic disturbances.

IMPORTANCE

Understanding the temporal turnover and stability of biotic communities is crucial for predicting the responses of sediment ecosystems to dredging disturbance. Most studies to date focused on the bacterial or macrobenthic community, only at two discontinuous time points, before and after dredging, and hence, it was difficult to analyze the community succession. This study first compared the stabilities and temporal changes of sediment bacterial, microeukaryotic, and macrobenthic communities at a continuous time course. The results showed that discordant responses of the three communities are mainly related to their different biological inherent attributes, and sensitivities to sediment geochemical variables change with dredging, resulting in changes in sediment ecosystem multifunctionality.

Onshore-offshore gradient in metacommunity turnover emerges only over macroevolutionary time-scales

Invertebrate lineages tend to originate and become extinct at a higher rate in onshore than in offshore habitats over long temporal durations (more than 10 Myr), but it remains unclear whether this pattern scales down to durations of stages (less than 5 Myr) or even sequences (less than 0.5 Myr). We assess whether onshore-offshore gradients in long-term turnover between the tropical Eocene and the warm-temperate Plio-Pleistocene can be extrapolated from gradients in short-term turnover, using abundances of molluscan species from bulk samples in the northeast Atlantic Province. We find that temporal turnover of metacommunities does not significantly decline with depth over short durations (less than 5 Myr), but significantly declines with depth between the Eocene and Plio-Pleistocene (approx. 50 Myr). This decline is determined by a higher onshore extinction of Eocene genera and families, by a higher onshore variability in abundances of genera and families, and by an onshore expansion of genera and families that were frequent offshore in the Eocene. Onshore-offshore decline in turnover thus emerges only over long temporal durations. We suggest that this emergence is triggered by abrupt and spatially extensive climatic or oceanographic perturbations that occurred between the Eocene and Plio-Pleistocene. Plio-Pleistocene metacommunities show a high proportion of bathymetric generalists, in contrast to Eocene metacommunities. Accordingly, the net cooling and weaker thermal gradients may have allowed offshore specialists to expand into onshore habitats and maintain their presence in offshore habitats.

Landscape fragmentation affects responses of avian communities to climate change

Forecasting the consequences of climate change is contingent upon our understanding of the relationship between biodiversity patterns and climatic variability. While the impacts of climate change on individual species have been well-documented, there is a paucity of studies on climate-mediated changes in community dynamics. Our objectives were to investigate the relationship between temporal turnover in avian biodiversity and changes in climatic conditions and to assess the role of landscape fragmentation in affecting this relationship. We hypothesized that community turnover would be highest in regions experiencing the most pronounced changes in climate and that these patterns would be reduced in human-dominated landscapes. To test this hypothesis, we quantified temporal turnover in avian communities over a 20-year period using data from the New York State Breeding Atlases collected during 1980-1985 and 2000-2005. We applied Bayesian spatially varying intercept models to evaluate the relationship between temporal turnover and temporal trends in climatic conditions and landscape fragmentation. We found that models including interaction terms between climate change and landscape fragmentation were superior to models without the interaction terms, suggesting that the relationship between avian community turnover and changes in climatic conditions was affected by the level of landscape fragmentation. Specifically, we found weaker associations between temporal turnover and climatic change in regions with prevalent habitat fragmentation. We suggest that avian communities in fragmented landscapes are more robust to climate change than communities found in contiguous habitats because they are comprised of species with wider thermal niches and thus are less susceptible to shifts in climatic variability. We conclude that highly fragmented regions are likely to undergo less pronounced changes in composition and structure of faunal communities as a result of climate change, whereas those changes are likely to be greater in contiguous and unfragmented habitats.