The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Although it is generally acknowledged that invasions by exotic plant species represent a major threat to biodiversity and ecosystem stability, little attention has been paid to the potential impacts of these invasions on nutrient cycling processes in the soil. The literature on plant–soil interactions strongly suggests that the introduction of a new plant species, such as an invasive exotic, has the potential to change many components of the carbon (C), nitrogen (N), water, and other cycles of an ecosystem. I have reviewed studies that compare pool sizes and flux rates of the major nutrient cycles in invaded and noninvaded systems for invasions of 56 species. The available data suggest that invasive plant species frequently increase biomass and net primary production, increase N availability, alter N fixation rates, and produce litter with higher decomposition rates than co-occurring natives. However, the opposite patterns also occur, and patterns of difference between exotics and native species show no trends in some other components of nutrient cycles (for example, the size of soil pools of C and N). In some cases, a given species has different effects at different sites, suggesting that the composition of the invaded community and/or environmental factors such as soil type may determine the direction and magnitude of ecosystem-level impacts. Exotic plants alter soil nutrient dynamics by differing from native species in biomass and productivity, tissue chemistry, plant morphology, and phenology. Future research is needed to (a) experimentally test the patterns suggested by this data set; (b) examine fluxes and pools for which few data are available, including whole-site budgets; and (c) determine the magnitude of the difference in plant characteristics and in plant dominance within a community that is needed to alter ecosystem processes. Such research should be an integral component of the evaluation of the impacts of invasive species.

Effects of Exotic Plant Invasions on Soil Nutrient Cycling Processes

Although the impacts of exotic plant invasions on community structure and ecosystem processes are well appreciated, the pathways or mechanisms that underlie these impacts are poorly understood. Better exploration of these processes is essential to understanding why exotic plants impact only certain systems, and why only some invaders have large impacts. Here, we review over 150 studies to evaluate the mechanisms underlying the impacts of exotic plant invasions on plant and animal community structure, nutrient cycling, hydrology and fire regimes. We find that, while numerous studies have examined the impacts of invasions on plant diversity and composition, less than 5% test whether these effects arise through competition, allelopathy, alteration of ecosystem variables or other processes. Nonetheless, competition was often hypothesized, and nearly all studies competing native and alien plants against each other found strong competitive effects of exotic species. In contrast to studies of the impacts on plant community structure and higher trophic levels, research examining impacts on nitrogen cycling, hydrology and fire regimes is generally highly mechanistic, often motivated by specific invader traits. We encourage future studies that link impacts on community structure to ecosystem processes, and relate the controls over invasibility to the controls over impact.

/pdf/mechanisms-underlying-the-impacts-of-exotic-plant-invasions-orvbpz9rpm.pdf

Mechanisms underlying the impacts of exotic plant invasions

When introduced to new habitats by humans, some plant species become much more dominant. This is primarily attributed to escape from specialist consumers. Release from these specialist enemies is also thought by some to lead to the evolution of increased competitive ability, driven by a decrease in the plant's resource allocation to consumer defense and an increase in allocation to size or fecundity. Here, we discuss a new theory for invasive success – the “novel weapons hypothesis”. We propose that some invaders transform because they possess novel biochemical weapons that function as unusually powerful allelopathic agents, or as mediators of new plant–soil microbial interactions. Root exudates that are relatively ineffective against their natural neighbors because of adaptation, may be highly inhibitory to newly encountered plants in invaded communities. In other words, the novel weapons of some plant invaders provide them with an advantage that may arise from differences in the regional coevolutionary ...

/pdf/novel-weapons-invasive-success-and-the-evolution-of-34vpfbpl72.pdf

Novel Weapons: Invasive Success and the Evolution of Increased Competitive Ability

Exotic species affect the biogeochemical pools and fluxes of materials and energy, thereby altering the fundamental structure and function of their ecosystems. Rapidly accumulating evidence from many species of both animal and plant invaders suggests that invasive species often increase pool sizes, particularly of biomass, and promote accelerated flux rates, but many exceptions can be found. Ecosystem dynamics are altered through a variety of interacting, mutually reinforcing mechanistic pathways, including species’ resource acquisition traits; population densities; ability to engineer changes to physical environmental conditions; effects on disturbance, especially fire; regimes; the ability to structure habitat for other species; and their impact on food webs. Local factors of landscape setting, history, and other sources of disturbance constrain ecosystem responses to invasions. New research directions are suggested, including the need for whole-system budgets, the quantification of abundance-impact relationships for particular ecosystem processes, and a better exploration of food web impacts on ecosystem processes.

Ecosystem Consequences of Biological Invasions

Exotic plant species are increasingly becoming the focus of research and have been identified as a component of human-induced global change. Successful invaders may alter soil conditions, but the effect of exotic species on soil microbial communities has not been studied. We studied two exotic understory plant species (Japanese barberry [Berberis thunbergii] and Japanese stilt grass [Microstegium vimineum]) in hardwood forests in northern New Jersey, USA. We sampled bulk and rhizosphere soils under the two exotic species, as well as under a co-occurring native species (blueberry [Vaccinium spp.]). We indexed the structure (by measuring phospholipid fatty acid [PLFA] profiles) and function (by measuring enzyme activities and substrate-induced respiration [SIR] profiles) of microbial communities in the sampled soils. Soils under the three species differed in microbial community structure and function. These differences were observed in both the rhizosphere and bulk soil samples. Differences in the structural variables were correlated to differences in the functional variables as demonstrated by canonical correlation analysis. These results indicate that successful exotic invasive species can have profound effects on the microbial community of the soil.

Exotic plant species alter the microbial community structure and function in the soil

Eastern deciduous forests have been invaded by two exotic species that often dominate the understory vegetation. Berberis thunbergii, a woody shrub, forms dense thickets, while Microstegium vimineum, a C4 grass, forms continuous lawns; the two species often co-occur. We hypothesized that a variety of characteristics of the exotic species may cause soil-based ecosystem processes to change following invasion, and that such changes could establish positive feedback processes that enhance the spread of the exotic. We examined changes in soil pH, nitrogen cycling, and litter dynamics in stands infested with both species in three locations in northern New Jersey (USA). Soils directly beneath each of the two exotics had higher pH values and higher nitrification rates and often had higher net N mineralization rates than did soils beneath adjacent patches of the most common native understory shrub, Vaccinium pallidum. These differences could be replicated in the greenhouse by growing the exotics in previously unin...

https://www.jstor.org/stable/info/3060920

Changes in soil functions following invasions of exotic understory plants in deciduous forests

Invasions of exotic plant species are among the most pervasive and important threats to natural ecosystems, however, the effects of plant invasions on soil processes and the soil biota have rarely been investigated. We grew two exotic and a native under-story plant species in the same mineral soil from a non-invaded forest stand in order to test whether observed differences in the field could be experimentally produced in the greenhouse. We characterized changes in the soil microbial community structure (as indexed by PLFAs) and function (as indexed by enzyme activities and SIR), as well as changes in potential nitrogen mineralization rates. We found that the invasion of two very dissimilar exotic species into the under-story of deciduous forests in eastern North America can rapidly cause changes in most of the studied soil properties. At the end of the three-month incubation, soils under the exotic species had significantly different PLFA, enzyme and SIR profiles than both initial soils and soils where native shrubs had been grown. We also observed a significant increase in pH and nitrification rates under one of the exotic plants. Such changes in the soil are potentially long-term (e.g. changes in soil pH) and are therefore likely to promote the re-invasion of these and other exotics. Both management of exotic plant invasions and the restoration of native communities must take into account exotic species effects on the soil.

Experimental analysis of the effect of exotic and native plant species on the structure and function of soil microbial communities.

Invasions by exotic plant species can alter ecosystem properties, including important soil functions and characteristics. As a result, decomposition of litter from the exotic, as well as native plants, can also be altered, leading to more profound changes in ecosystem functioning. We present here a study of eight enzyme activities during the decomposition of litter from four plant species, two of which are successful exotic invaders in Northeastern USA deciduous forests. The four studied species are: Japanese barberry (exotic), Japanese stilt grass (exotic), chestnut oak (native) and black birch (native). We measured enzyme activities in the decomposing litter at two locations (exotics infested and native vegetation) in two parks in Northeastern New Jersey. In the first 2 years of decomposition, patterns of enzyme activites changed significantly among the four types of litter, however, they were not affected by the location (exotic/native) where decomposition was taking place. Our results clearly show that litter chemistry and site characteristics are strong determinants of enzyme activity in decomposing litter. The microbial community in the litter quickly adapted to the differences in litter chemistry, as patterns of enzyme activity in decomposing litter from the two exotic species were virtually indistinguishable between exotic and native locations.

Enzyme activities during litter decomposition of two exotic and two native plant species in hardwood forests of New Jersey

Two exotic plant species, Berberis thunbergii and Microstegium vimineum, recently have invaded deciduous hardwood forests in the Northeast. We examined changes in soil properties that maybe associated with this invasion in three parks in northern New Jersey. In each park, we collected soil and vegetation data along transects that were established across heavily infested areas and extended into uninvaded forest. The data were analyzed statistically by ANOVA and Canonical Correspondence Analysis (CCA). Significant differences were found between invaded and uninvadcd plots in both soil and vegetation characteristics. Invaded areas have fewer oaks (Quercus spp.) in the canopy, and lack the native understory shrubs (Vaccinium spp.). The pH of soils in the invaded areas is significantly higher than in the uninvaded areas, and the litter and organic horizons are thinner. The data cannot show that the exotic species have caused these changes. However, the occurrence of contrasting soils in adjacent areas of native vegetation, with no evidence of differences in land-use history between areas, suggests that such a cause-and-effect relationship exists. We propose a feedback loop involving the exotic plants, and the presence of earthworms to explain these dramatic soil differences.

Peter Stefanov Kourtev

Papers

Exotic plant species alter the microbial community structure and function in the soil

Changes in soil functions following invasions of exotic understory plants in deciduous forests

Experimental analysis of the effect of exotic and native plant species on the structure and function of soil microbial communities.

Enzyme activities during litter decomposition of two exotic and two native plant species in hardwood forests of New Jersey

Effects of exotic plant species on soil properties in hardwood forests of New Jersey.