Genes to ecosystems: exploring the frontiers of ecology with one of the smallest biological units

Genes and their expression levels in individual species can structure whole communities and affect ecosystem processes. Although much has been written about community and ecosystem phenotypes with a few model systems, such as poplar and goldenrod, here we explore the potential application of a community genetics approach with systems involving invasive species, climate change and pollution. We argue that community genetics can reveal patterns and processes that otherwise might remain undetected. To further facilitate the community genetics or genes-to-ecosystem concept, we propose four community genetics postulates that allow for the conclusion of a causal relationship between the gene and its effect on the ecosystem. Although most current studies do not satisfy these criteria completely, several come close and, in so doing, begin to provide a genetic-based understanding of communities and ecosystems, as well as a sound basis for conservation and management practices.     

Parasites, disease and the structure of ecological communities

Pathogens and parasites are fascinating to epidemiologists and ecologists alike; as well as causing disease in individual species, they can perturb the normal functioning of a community and thus give insights into the way that the community 'functions' Several recent studies on diseases in animal populations have confirmed the importance of pathogens and parasites as components of ecological systems, while also revealing the underlying structure of complex multispecies communities.     

All together now: experimental multispecies biofilm model systems

Studies of microorganisms have traditionally focused on single species populations, which have greatly facilitated our understanding of the genetics and physiology that underpin microbial growth, adaptation and biofilm development. However, given that most microorganisms exist as multispecies consortia, the field is increasingly exploring microbial communities using a range of technologies traditionally limited to populations, including meta‐omics based approaches and high resolution imaging. The experimental communities currently being explored range from relatively low diversity, for example, two to four species, to significantly more complex systems, comprised of several hundred species. Results from both defined and undefined communities have revealed a number of emergent properties, including improved stress tolerance, increased biomass production, community level signalling and metabolic cooperation. Based on results published to date, we submit that community‐based studies are timely and increasingly reveal new properties associated with multispecies consortia that could not be predicted by studies of the individual component species. Here, we review a range of defined and undefined experimental systems used to study microbial community interactions.     

The life-history impact and implications of multiple parasites for bumble bee queens

Most studies of the consequences of parasitism on fitness have examined single host–parasite systems. However, parasitological studies show that most hosts are constantly challenged by a complex parasite community. Thus, neither the response of hosts to individual parasite species nor the individual impact of these parasite species is likely to be as unconstrained as studies of single host–parasite systems might suggest. In this study, the parasite community structure in spring queens of the common European bumble bee, Bombus pratorum, was assessed. By capturing queens and allowing them to rear colonies in the laboratory, the relative impact of different parasite species on fitness across the annual host life-cycle could be examined. Of 160 queens, 67% were parasitised by one or more members of a five-species parasite community. The impact of parasites varied from being highly virulent to undetectable under benign laboratory conditions. The majority of multi-parasite infections involved a high impact parasite, which resulted in the removal of associated parasites from the host population. This study shows that, whilst multiple infections occur within individual hosts, most parasites act individually on their hosts. However, multiple parasite species in the host population may constrain the host population’s ability to adapt to single parasite species.     

Fungal volatiles mediate cheese rind microbiome assembly

In vitro studies in plant, soil, and human systems have shown that microbial volatiles can mediate microbe–microbe or microbe–host interactions. These previous studies have often used artificially high concentrations of volatiles compared to in situ systems and have not demonstrated the roles volatiles play in mediating community-level dynamics. We used the notoriously volatile cheese rind microbiome to identify bacteria responsive to volatiles produced by five widespread cheese fungi. Vibrio casei had the strongest growth stimulation when exposed to all fungi. In multispecies community experiments, fungal volatiles caused a shift to a Vibrio-dominated community, potentially explaining the widespread occurrence of Vibrio in surface-ripened cheeses. RNA sequencing identified activation of the glyoxylate shunt as a possible mechanism underlying volatile-mediated growth promotion and community assembly. Our study demonstrates how airborne chemicals could be used to control the composition of microbiomes and illustrates how volatiles may impact the development of cheese rinds.     

植被群落特征对城市生态系统服务的影响研究进展

生态空间（林地、灌木、草地、水体）所产生的生态系统服务极大的改善了人类的生存环境,在城市绿地破碎化日益严重、绿地质量逐渐降低、乡土植物逐渐减少、入侵风险逐渐加剧等生态背景下,如何维持稳定而持续增长的城市生态系统服务供给,一直困扰着当下从事城市生态学领域研究的学者和城市管理者。植被群落作为城市绿地系统的基本组成单元,在绿地破碎化趋势下,可作为研究内容来探讨城市生态系统服务维持或提升策略;植被群落泛指城市中常见的、具有明显边界的、按照一定分布规则的植物群落单元,既包括道路绿地、居住区绿地、公园绿地等,也包括城市郊野自然林地。但对植被群落生态功能的研究也多停留在对某一生态问题的简单相关性研究,缺乏系统性和整体性。从微观层面的植被群落角度,整合相关文献研究,介绍了受植被群落特征影响的6种典型城市生态系统服务,综述了植被群落特征对这6种城市生态系统服务的影响机理,对植被群落特征因子进行总结、归类,从树种特性、垂直结构、水平结构、其他4个角度构建了"植被群落特征因子对城市生态系统服务影响关系表"。最后面向典型生态系统服务提升提出了城市低质量植被群落地区的营建和更新原则,以期为今后城市园林部门、规划部门制定城市绿地系统规划提供基础性技术支撑。     

High-throughput DNA barcoding for ecological network studies

The network theoretical framework of ecological community studies is expected to promote not only the basic understanding of ecological and coevolutionary dynamics but also the application of those scientific insights into ecosystem management. However, our knowledge of ecological network architecture in the wild largely stems from empirical studies on macro-organismal systems such as those of plant–pollinator, plant–seed disperser, and prey–predator interactions. In this sense, we have remained ignorant of the diversity of ecological network architecture, its underlying assembly processes, and its consequences on ecological and coevolutionary dynamics. In this paper, I discuss how the high-throughput DNA barcoding of microbes, especially that based on next-generation sequencing, potentially expands the target of ecological network studies. I review the methodological platforms of next-generation sequencing-based analyses of microbe–host animal/plant networks and then introduce some case studies on the networks of plants and their hyper-diverse fungal symbionts. As those preliminary studies are uncovering the unexpected diversity of ecological network architecture, further application of such next-generation sequencing-based analyses to a diverse array of microbial systems will significantly improve our views on community ecological and coevolutionary processes.     

Aquatic islands in the sky: 100 years of research on water‐filled tree holes

Water‐filled tree holes are unique ecosystems that may occur high up in tree crowns and are essentially aquatic islands in the sky. Insect larvae, mesofauna, and other organisms colonize the waterbodies and feed on the accumulating detritus. Water‐filled tree holes are not only important habitats for these species but have been used as model systems in ecology. Here, we review more than 100 years of research on tree‐hole inhabiting organisms and show that most studies focus on selected or even single species (most of which are mosquitoes), whereas only few studies examine groups other than insects, especially in the tropics. Using a vote counting of results and a meta‐analysis of community studies, we show that the effects of tree‐hole size and resources on abundance and richness were investigated most frequently. Both were found to have a positive effect, but effect sizes were modulated by site‐specific environmental variables such as temperature or precipitation. We also show that parameters such as the height of the tree holes above ground, tree‐hole density, predation, and detritus type can be important drivers of organism abundance or richness but are less often tested. We identify several important research gaps and potential avenues for future research. Specifically, future studies should investigate the structure, functions, and temporal dynamics of tree‐hole food webs and their cross‐system interactions, for example, with terrestrial predators that act as a connection to their terrestrial surroundings in meta‐ecosystems. Global observational or experimental tree‐hole studies could contribute pivotal information on spatial variation of community structure and environmental drivers of community assembly. With a better understanding of these unique aquatic habitats in terrestrial ecosystems, natural and artificial tree holes can not only serve as model systems for addressing fundamental ecological questions but also serve as indicator systems of the impacts of environmental change on ecosystems.     

Influence of Algal Community Structure on Denitrification Rates in Periphyton Cultivated on Artificial Substrata

We conducted a field survey of periphyton cultivated on benthic mesh installations in freshwater aquatic systems, including two constructed wetlands and a pond, and also studied periphyton grown on a benthic mesh in laboratory mesocosms. The objectives of this study were to (1) determine if periphyton cultivated on benthic mesh denitrifies at higher rates than the underlying sediments and (2) determine if denitrification rates within periphyton vary with characteristics such as algal and bacterial community structure and biomass. We measured denitrification potential rates of field and laboratory periphyton by the acetylene inhibition method. We characterized algal community composition by algal identification and bacterial community composition by terminal restriction fragment length polymorphisms. Periphyton collected on benthic mesh from our field sites denitrified at significantly higher rates than the underlying sediments, regardless of sampling site or season. Results from both our field survey and laboratory studies indicated a significant, positive correlation between diatom presence and denitrification rate. In our laboratory studies, we found that periphyton with the highest diatom abundance showed the highest denitrification rates as well as a distinct bacterial community composition. These results suggest a synergistic relationship between diatoms and denitrifying bacteria that warrants further study.     

Species richness–variability relationships in multi-trophic aquatic microcosms

While species loss may affect the temporal variability of populations and communities differently in multi- versus single-trophic level communities, the nature of these differences are poorly understood. Here, we report on an experiment where we manipulated species richness of multi-trophic rock pool invertebrate communities to determine the effects of species richness, S, on the temporal variability of communities, populations, and individual species. As in single-trophic level studies, temporal variability in community abundance decreased with increasing species richness. However, in contrast to most studies in single-trophic level systems, temporal variability of populations also decreased as species richness increased. Furthermore, the variability of the constituent populations strongly correlated with variability of community abundance suggesting that, in rock pools, S affects community variability through its stabilizing effect on component populations. Our results suggest that species loss may affect population and community variability differently in multi-trophic versus single trophic level communities. If this is so, then the mechanisms proposed to underlie the effects of S on community variability in single-trophic communities may have to be supplemented by those that describe contributions to population stability in order to fully describe the patterns observed in multi-trophic communities.     

An evaluation of periphyton community structure and function on tile and cobble substrata in experimental stream mesocosms

Periphyton communities are an ecologically important source of information when conducting experimental stream ecotoxicological studies. Experimental stream studies often utilize unreplicated systems in order to understand dose-response phenomena. The objective of this study was to examine the robustness of such a dose-response investigation. Autotrophic and heterotrophic periphyton were evaluated in replicated control experimental streams with open recruitment (once-through flow design). Measurements of population and community structure and community function over an eleven week colonization period were made on unglazed clay tile and cobble substrata. Several measures were significantly different during the study; however, most of these were a result of initial stochastic colonization events or associated with relatively rare algal populations. During the latter half of the study autotrophic and heterotrophic community measurements on tile and cobble substrata displayed similar trends in both control streams. Population and community metrics were significantly different for approximately 5% of the 400 measurements made after the initial sampling. These results strongly suggest that the driving forces behind structuring aquatic population and community responses will be test chemical exposure and not spuriously developed stream ecosystems with individual trajectories. Recruitment in these open systems is evenly distributed across the replicated experimental stream ecosystems.     

Marine range shifts and species introductions: comparative spread rates and community impacts

Aim Shifts in species ranges are a predicted and realized effect of global climate change; however, few studies have addressed the rates and consequence of such shifts, particularly in marine systems. Given ecological similarities between shifting and introduced species, we examined how our understanding of range shifts may be informed by the more established study of non‐native species introductions. Location Marine systems world‐wide. Methods Database and citation searches were used to identify 129 marine species experiencing range shifts and to determine spread rates and impacts on recipient communities. Analyses of spread rates were based on studies for which post‐establishment spread was reported in linear distance. The sizes of the effects of community impacts of shifting species were compared with those of functionally similar introduced species having ecologically similar impacts. Results Our review and meta‐analyses revealed that: (1) 75% of the range shifts found through the database search were in the poleward direction, consistent with climate change scenarios, (2) spread rates of range shifts were lower than those of introductions, (3) shifting species spread over an order of magnitude faster in marine than in terrestrial systems, and (4) directions of community effects were largely negative and magnitudes were often similar for shifters and introduced species; however, this comparison was limited by few data for range‐shifting species. Main conclusions Although marine range shifts are likely to proceed more slowly than marine introductions, the community‐level effects could be as great, and in the same direction, as those of introduced species. Because it is well‐established that introduced species are a primary threat to global biodiversity, it follows that, just like introductions, range shifts have the potential to seriously affect biological systems. In addition, given that ranges shift faster in marine than terrestrial environments, marine communities might be affected faster than terrestrial ones as species shift with climate change. Regardless of habitat, consideration of range shifts in the context of invasion biology can improve our understanding of what to expect from climate change‐driven shifts as well as provide tools for formal assessment of risks to community structure and function.     

In vitro model systems for exploring oral biofilms: From single-species populations to complex multi-species communities

Numerous in vitro biofilm model systems are available to study oral biofilms. Over the past several decades, increased understanding of oral biology and advances in technology have facilitated more accurate simulation of intraoral conditions and have allowed for the increased generalizability of in vitro oral biofilm studies. The integration of contemporary systems with confocal microscopy and 16S rRNA community profiling has enhanced the capabilities of in vitro biofilm model systems to quantify biofilm architecture and analyse microbial community composition. In this review, we describe several model systems relevant to modern in vitro oral biofilm studies: the constant depth film fermenter, Sorbarod perfusion system, drip–flow reactor, modified Robbins device, flowcells and microfluidic systems. We highlight how combining these systems with confocal microscopy and community composition analysis tools aids exploration of oral biofilm development under different conditions and in response to antimicrobial/anti-biofilm agents. The review closes with a discussion of future directions for the field of in vitro oral biofilm imaging and analysis.     

Application of the microbial community coalescence concept to riverine networks

Flows of water, soil, litter, and anthropogenic materials in and around rivers lead to the mixing of their resident microbial communities and subsequently to a resultant community distinct from its precursors. Consideration of these events through a new conceptual lens, namely, community coalescence, could provide a means of integrating physical, environmental, and ecological mechanisms to predict microbial community assembly patterns better in these habitats. Here, we review field studies of microbial communities in riverine habitats where environmental mixing regularly occurs, interpret some of these studies within the community coalescence framework and posit novel hypotheses and insights that may be gained in riverine microbial ecology through the application of this concept. Particularly in the face of a changing climate and rivers under increasing anthropogenic pressures, knowledge about the factors governing microbial community assembly is essential to forecast and/or respond to changes in ecosystem function. Additionally, there is the potential for microbial ecology studies in rivers to become a driver of theory development: riverine systems are ideal for coalescence studies because regular and predictable environmental mixing occurs. Data appropriate for testing community coalescence theory could be collected with minimal alteration to existing study designs.     

Extracellular enzymes in terrestrial, freshwater, and marine environments: perspectives on system variability and common research needs

Extracellular enzymes produced by heterotrophic microbial communities are major drivers of carbon and nutrient cycling in terrestrial, freshwater, and marine environments. Although carbon and nutrient cycles are coupled on global scales, studies of extracellular enzymes associated with terrestrial, freshwater, and marine microbial communities are not often compared across ecosystems. In part, this disconnect arises because the environmental parameters that control enzyme activities in terrestrial and freshwater systems, such as temperature, pH, and moisture content, have little explanatory power for patterns of enzyme activities in marine systems. Instead, factors such as the functional diversity of microbial communities may explain varying patterns of enzyme activities observed in the ocean to date. In any case, many studies across systems focus on similar issues that highlight the commonalities of microbial community organization. Examples include the effective lifetime of enzymes released into the environment; the extent to which microbial communities coordinate enzyme expression to decompose complex organic substrates; and the influence of microbial community composition on enzyme activities and kinetics. Here we review the often-disparate research foci in terrestrial, freshwater, and marine environments. We consider the extent to which environmental factors may regulate extracellular enzyme activities within each ecosystem, and highlight commonalities and current methodological challenges to identify research questions that may aid in integrating cross-system perspectives in the future.     

Biomass-dependent susceptibility to drought in experimental grassland communities

Earlier studies indicated that plant diversity influences community resistance in biomass when ecosystems are exposed to perturbations. This relationship remains controversial, however. Here we constructed grassland communities to test the relationships between species diversity and productivity under control and experimental drought conditions. Species richness was not correlated with biomass either under constant conditions or under drought conditions. However, communities with lower biomass production were more resistant to drought stress than those that were more productive. Our results also showed that ecosystem resistance to drought is a decreasing but nonlinear function of biomass. In contrast, species diversity had little and an equivocal effect on ecosystem resistance. From the results reported here, and the results of several previous studies, we suggest that high biomass systems exhibited a greater biomass reduction in response to drought than low biomass systems did, regardless of the relationship between plant diversity and community biomass production.     

Discovering Link Communities in Complex Networks by an Integer Programming Model and a Genetic Algorithm

Identification of communities in complex networks is an important topic and issue in many fields such as sociology, biology, and computer science. Communities are often defined as groups of related nodes or links that correspond to functional subunits in the corresponding complex systems. While most conventional approaches have focused on discovering communities of nodes, some recent studies start partitioning links to find overlapping communities straightforwardly. In this paper, we propose a new quantity function for link community identification in complex networks. Based on this quantity function we formulate the link community partition problem into an integer programming model which allows us to partition a complex network into overlapping communities. We further propose a genetic algorithm for link community detection which can partition a network into overlapping communities without knowing the number of communities. We test our model and algorithm on both artificial networks and real-world networks. The results demonstrate that the model and algorithm are efficient in detecting overlapping community structure in complex networks.     

A theoretical basis for the study of predatory syrphid fly ecology

Predacious syrphid fly species, also known as flower flies or hover flies, are cosmopolitan diptera that play two important ecological roles: predator and pollinator. In decades past, syrphid flies were studied by agricultural researchers due to their larvae’s ability to function as a biological control agent. In recent years, the global decline in both honey bees and various important wild bee species has led ecological researchers to investigate the role of syrphid fly pollination in both natural systems and agriculture. While these two roles have often been considered separately, they are rarely considered together in single studies. Syrphid fly population fluctuations in natural and agricultural systems are understudied, prompting calls for further study into the fundamental drivers of population dynamics of syrphid communities. In order to develop a deeper understanding of the fundamental dynamics of syrphid ecology, the present study offers a community model where both syrphid predation and pollination are incorporated into a single dynamic model. Using populations of predacious syrphid flies, herbivorous insects, and a shared resource flowering plant, the model is used to investigate community dynamics and persistence across different levels of plant reproductive dependence on syrphid pollination. Results indicate distinct levels of community viability across different pollination relationships as well as a tendency toward chaotic dynamics inherent to the trophic interactions of the community.