Linking Community and Ecosystem Processes: The Role of Minor Species

Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments

Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.

Grazing and precipitation addition reduces the temporal stability of aboveground biomass in a typical steppe of Chinese Loess Plateau

Few studies on the effects of human activities and global climate change on temporal stability have considered either grazing or precipitation addition (PA). How community stability responds to the interaction between PA and grazing in a single experiment remains unknown. We studied the impact of grazing and PA on the temporal stability of communities in four years field experiment conducted in a typical steppe, adopting a randomized complete block design with grazing was the main block factor and PA was the split block factor. Grazing and PA had negative impacts on the temporal stability of communities. PA reduced the community stability through decreasing the stability of subordinate and community species richness (SR), whereas grazing reduced the community stability through decreasing the stability of the SR and dominant species. In contrast, grazing and PA maintained community stability through increasing species asynchronism and promoting the decoupling of asynchronism and stability. Our results revealed the different mechanisms of grazing and PA on community stability. Exploring the response characteristics of population dynamics to global climate change and pasture management is key to understanding future climate scenarios and changes in community stability under grazing.

Demystifying dominant species

The pattern of a few abundant species and many rarer species is a defining characteristic of communities worldwide. These abundant species are often referred to as dominant species. Yet, despite their importance, the term dominant species is poorly defined and often used to convey different information by different authors. Based on a review of historical and contemporary definitions we develop a synthetic definition of dominant species. This definition incorporates the relative local abundance of a species, its ubiquity across the landscape, and its impact on community and ecosystem properties. A meta-analysis of removal studies shows that the loss of species identified as dominant by authors can significantly impact ecosystem functioning and community structure. We recommend two metrics that can be used jointly to identify dominant species in a given community and provide a roadmap for future avenues of research on dominant species. In our review, we make the case that the identity and effects of dominant species on their environments are key to linking patterns of diversity to ecosystem function, including predicting impacts of species loss and other aspects of global change on ecosystems.

Competition for microsites during recruitment in semiarid annual plant communities

The concept of microsites for recruitment is central to plant ecology, but it is unclear whether these sites are abstract constructs or real entities. I hypothesize that, in generally microsite-limited communities, microsites comprise a limiting physical resource for which different species compete. I tested this hypothesis on winter-annual communities on biocrust in the semiarid Northern Negev of Israel, in which most species are microsite-limited, while the dominant grass (Stipa capensis) has overcome this limitation by efficient microsite acquisition and a lack of secondary seed dormancy. I tested whether the dominant suppresses the subordinate species, collectively, during recruitment, rather than during growth. To this end, I conducted a field experiment with three blocks of six plots (6 m × 6 m) with two treatments - mowing in spring 2006 (intershrub, intershrub + shrub patches, and none) and shrub-patch removal (0% or 50% of the patches). I collected data from four seed traps per plot before spring 2007 and from five plant samples per plot at the end of spring. Mowing significantly reduced both seed and plant density of the dominant species, reflecting seed-limited recruitment, and increased subordinate plant density by competitive release. Multiple regressions of per-plant and per-gram effects and responses showed that competition was a direct effect of the dominant's density. Total and per-group biomass was proportional to density, implying density-independent per capita growth. Subordinate species number also increased with their density, due to the sample-size effect. These findings indicate that the seed-limited dominant diffusely suppresses the subordinates during recruitment, supporting the microsite competition hypothesis. The shift from growth resources to microsites extends the role of inter-specific competition along productivity and disturbance gradients, and highlights the asymmetric relationship between the two kinds of competition, as microsite competition is only observable if initial abundances are not overshadowed by density-dependent growth and mortality. The findings also demonstrate that (1) lacking secondary seed dormancy is an evolutionarily stable strategy in dryland annuals, alongside seed dormancy in microsite-limited species, and (2) biomass removal (e.g., by herbivory) increases small-scale biodiversity, enhancing the sustainability of dryland grazing, but without compensatory growth.

Interactions among salt marsh plants vary geographically but not latitudinally along the California coast

The strength of species interactions often varies geographically and locally with environmental conditions. Competitive interactions are predicted to be stronger in benign environments while facilitation is expected to be stronger in harsh ones. We tested these ideas with an aboveground neighbor removal experiment at six salt marshes along the California coast. We determined the effect of removals of either the dominant species, Salicornia pacifica, or the subordinate species on plant cover, aboveground biomass and community composition, as well as soil salinity and moisture. We found that S. pacifica consistently competed with the subordinate species and that the strength of competition varied among sites. In contrast with other studies showing that dominant species facilitate subordinates by moderating physical stress, here the subordinate species facilitated S. pacifica shortly after removal treatments were imposed, but the effect disappeared over time. Contrary to expectations based on patterns observed in east coast salt marshes, we did not see patterns in species interactions in relation to latitude, climate, or soil edaphic characteristics. Our results suggest that variation in interactions among salt marsh plants may be influenced by local‐scale site differences such as nutrients more than broad latitudinal gradients.

Hill number as a bacterial diversity measure framework with high-throughput sequence data

Bacterial diversity is an important parameter for measuring bacterial contributions to the global ecosystem. However, even the task of describing bacterial diversity is challenging due to biological and technological difficulties. One of the challenges in bacterial diversity estimation is the appropriate measure of rare taxa, but the uncertainty of the size of rare biosphere is yet to be experimentally determined. One approach is using the generalized diversity, Hill number (N_a), to control the variability associated with rare taxa by differentially weighing them. Here, we investigated Hill number as a framework for microbial diversity measure using a taxa-accmulation curve (TAC) with soil bacterial community data from two distinct studies by 454 pyrosequencing. The reliable biodiversity estimation was obtained when an increase in Hill number arose as the coverage became stable in TACs for a ≥ 1. In silico analysis also indicated that a certain level of sampling depth was desirable for reliable biodiversity estimation. Thus, in order to attain bacterial diversity from second generation sequencing, Hill number can be a good diversity framework with given sequencing depth, that is, until technology is further advanced and able to overcome the under- and random-sampling issues of the current sequencing approaches.

Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data

Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete-case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete-case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices.

Arbuscular mycorrhizal fungi reduce the differences in competitiveness between dominant and subordinate plant species

In grassland communities, plants can be classified as dominants or subordinates according to their relative abundances, but the factors controlling such distributions remain unclear. Here, we test whether the presence of the arbuscular mycorrhizal (AM) fungus Glomus intraradices affects the competitiveness of two dominant (Taraxacum officinale and Agrostis capillaris) and two subordinate species (Prunella vulgaris and Achillea millefolium). Plants were grown in pots in the presence or absence of the fungus, in monoculture and in mixtures of both species groups with two and four species. In the absence of G. intraradices, dominants were clearly more competitive than subordinates. In inoculated pots, the fungus acted towards the parasitic end of the mutualism-parasitism continuum and had an overall negative effect on the growth of the plant species. However, the negative effects of the AM fungus were more pronounced on dominant species reducing the differences in competitiveness between dominant and subordinate species. The effects of G. intraradices varied with species composition highlighting the importance of plant community to mediate the effects of AM fungi. Dominant species were negatively affected from the AM fungus in mixtures, while subordinates grew identically with and without the fungus. Therefore, our findings predict that the plant dominance hierarchy may flatten out when dominant species are more reduced than subordinate species in an unfavourable AM fungal relationship (parasitism).

Using dual classifications in the development of avian wetland indices of biological integrity for wetlands in West Virginia, USA

Considerable resources are being used to develop and implement bioassessment methods for wetlands to ensure that "biological integrity" is maintained under the United States Clean Water Act. Previous research has demonstrated that avian composition is susceptible to human impairments at multiple spatial scales. Using a site-specific disturbance gradient, we built avian wetland indices of biological integrity (AW-IBI) specific to two wetland classification schemes, one based on vegetative structure and the other based on the wetland's position in the landscape and sources of water. The resulting class-specific AW-IBI was comprised of one to four metrics that varied in their sensitivity to the disturbance gradient. Some of these metrics were specific to only one of the classification schemes, whereas others could discriminate varying levels of disturbance regardless of classification scheme. Overall, all of the derived biological indices specific to the vegetative structure-based classes of wetlands had a significant relation with the disturbance gradient; however, the biological index derived for floodplain wetlands exhibited a more consistent response to a local disturbance gradient. We suspect that the consistency of this response is due to the inherent nature of the connectivity of available habitat in floodplain wetlands.

Does species diversity limit productivity in natural grassland communities?

Theoretical analyses and experimental studies of synthesized assemblages indicate that under particular circumstances species diversity can enhance community productivity through niche complementarity. It remains unclear whether this process has important effects in mature natural ecosystems where competitive feedbacks and complex environmental influences affect diversity-productivity relationships. In this study, we evaluated diversity-productivity relationships while statistically controlling for environmental influences in 12 natural grassland ecosystems. Because diversity-productivity relationships are conspicuously nonlinear, we developed a nonlinear structural equation modeling (SEM) methodology to separate the effects of diversity on productivity from the effects of productivity on diversity. Meta-analysis was used to summarize the SEM findings across studies. While competitive effects were readily detected, enhancement of production by diversity was not. These results suggest that the influence of small-scale diversity on productivity in mature natural systems is a weak force, both in absolute terms and relative to the effects of other controls on productivity.

SHIFTS IN POSITIVE AND NEGATIVE PLANT INTERACTIONS ALONG A GRAZING INTENSITY GRADIENT

Isolating the single effects and net balance of negative and positive species effects in complex interaction networks is a necessary step for understanding community dynamics. Facilitation and competition have both been found to operate in harsh environments, but their relative strength may be predicted to change along gradients of herbivory. Moreover, facilitation effects through habitat amelioration and protection from herbivory may act together determining the outcome of neighborhood plant-plant interactions. We tested the hypothesis that grazing pressure alters the balance of positive and negative interactions between palatable and unpalatable species by increasing the strength of positive indirect effects mediated by associational resistance to herbivory. We conducted a two-year factorial experiment in which distance (i.e., spatial association) from the nearest unpalatable neighbor (Stipa speciosa) and root competition were manipulated for two palatable grasses (Poa ligularis and Bromus pictus), at three levels of sheep grazing (none, moderate, and high) in a Patagonian steppe community. We found that grazing shifted the effect of Stipa on both palatable grasses, from negative (competition) in the absence of grazing to positive (facilitation) under increasing herbivore pressure. In ungrazed sites, belowground competition was the dominant interaction, as shown by a significant reduction in performance of palatable grasses transplanted near to Stipa tussocks. In grazed sites, biomass of palatable plants was greater near than far from Stipa regardless of competition treatment. Proximity to Stipa reduced the amount of herbivory suffered by palatable grasses, an indirect effect that was stronger under moderate than under intense grazing. Our results demonstrate that facilitation, resulting mainly from protection against herbivory, is the overriding effect produced by unpalatable neighbors on palatable grasses in this rangeland community. This finding challenges the common view that abiotic stress amelioration should be the predominant type of facilitation in arid environments and highlights the role of herbivory in modulating complex neighborhood plant interactions in grazing systems.