Altered Species Composition Research Articles

Low-temperature induced leaf elements accumulation in aquatic macrophytes across Tibetan Plateau

The geographic patterns of leaf nutrients in different ecosystems have drawn great attention from stoichiometric ecologists. Two hypotheses, temperature–plant physiological hypothesis (TPPH) and temperature–biogeochemical hypothesis (TBH), were proposed to explain the effects of temperature on terrestrial plants nutrients concentrations and stoichiometry. However, the patterns and causes of variations in leaf C, N and P of aquatic plants in harsh environments have been less well addressed. We collected samples of 35 aquatic macrophyte species across the Tibetan Plateau. The relationships between leaf nutrients were tested and compared with previously published results from freshwater and terrestrial ecosystems and global datasets. We further examined the effects of environmental factors on leaf nutrients. The mean (and median) values of leaf C, N and P were 378.3 (385.0), 28.6 (28.6) and 2.8 (2.7)mgg−1, respectively, while the mass ratios of leaf C:N and N:P were 14.4 and 11.3, respectively. The three elements were positively correlated with each other, with the exception of C and P. The power law exponent relating N and P was 0.74, higher than the expectation of 2/3, which was derived from global data set, possibly due to disproportionate accumulation of leaf P. Phylogeny and temperature primarily explained the observed variations in leaf nutrient contents along environmental gradients, whereas the properties of water and sediments had a weak influence. As temperature decreased, leaf nutrient concentrations increased, but their ratios decreased. The leaf nutrient concentrations measured in this study were higher than those from warmer regions, indicating low temperature-induced nutrient accumulation, which is consistent with TPPH. Our results suggested that the plants concentrated N and P and expedited their growth rate to offset the stress induced by low temperatures and a short growing season on the Tibetan Plateau. Alteration in species composition primarily accounted for the variation in stoichiometric patterns of aquatic macrophytes. Low temperature controlled the stoichiometric patterns directly or indirectly via affecting the species composition along sufficient environmental gradients.

Aquaculture Disturbance Impacts the Diet but not Ecological Linkages of a Ubiquitous Predatory Fish

Aquaculture operations are a frequent and prominent cause of anthropogenic disturbance to marine and estuarine communities and may alter species composition and abundance. However, little is known about how such disturbances affect trophic linkages or ecosystem functions. In Puget Sound, Washington, aquaculture of the Pacific geoduck clam (Panopea generosa) is increasing and involves placing nets and polyvinyl chloride (PVC) tubes in intertidal areas to protect juvenile geoducks from predators. Initial studies of the structured phase of the farming cycle have documented limited impacts on the abundance of some species. To examine the effect of geoduck aquaculture on ecological linkages, the trophic relationships of a local ubiquitous consumer, Pacific staghorn sculpin (Leptocottus armatus), to its invertebrate prey were compared between geoduck aquaculture sites and nearby reference areas with no aquaculture. Mark-recapture data indicated that sculpin exhibit local site fidelity to cultured and reference areas. The stomach contents of sculpin and stable isotope signatures of sculpin and their prey were examined to study the trophic ecology of cultured and reference areas. Results showed that the structured phase of geoduck aquaculture initiated some changes to staghorn sculpin ecology, as reflected in sculpin diet through stomach content analysis. However, carbon and nitrogen stable isotopes revealed that the general food web function of sculpin remained unchanged. The source of carbon at the base of the food web and the trophic position of sculpin were not impacted by geoduck aquaculture. The study has important implications for geoduck aquaculture management and will inform regulatory decisions related to shellfish aquaculture policy.

Differential effects of two explosive compounds on seed germination and seedling morphology of a woody shrub, Morella cerifera.

Soils contaminated with explosive compounds occur on a global scale. Research demolition explosive (RDX) (hexahydro-1,3,5-trinitro-1,3,5-triazine) and trinitrotoluene (TNT) (2-methyl-1,3,5-trinitrobenzene) are the most common explosive compounds in the environment. These compounds, by variably impacting plant health, can affect species establishment in contaminated areas. Our objective was to quantify comparative effects of RDX and TNT on a woody shrub, Morella cerifera, commonly found on bombing ranges along the Atlantic Coast of the United States. Two life stages of M. cerifera, Seeds and juvenile plants, were exposed to soil amended with concentrations of RDX and TNT representative of field levels; RDX up to 1,500ppm and TNT up to 900ppm. Percent germination was recorded for 3weeks; morphological metrics of necrotic, reduced, and curled leaves, in addition to shoot length and number measured at the end of the experiment (8weeks) for juvenile plants. All concentrations of RDX inhibited seed germination while TNT did not have an effect at any concentration. As contaminant concentration increased, significant increases in seedling morphological damage occurred in the presence of RDX, whereas TNT did not affect seedling morphology at any concentration. Overall the plants were more sensitive to the presence of RDX. Species specific responses to explosive compounds in the soil have the potential to act as a physiological filter, altering plant recruitment and establishment. This filtering of species may have a number of large scale impacts including: altering species composition and ecological succession.

Turbidity influences trophic interactions in estuaries

We investigated how changes in abiotic conditions resulting from human activities indirectly alter trophic interactions using turbidity in estuaries as a model system. Development and nutrient input are causing turbidity to increase in many coastal areas. Using an 18 yr data set from Aransas and San Antonio Bays in Texas, we found fish abundance (Sciaenops ocellatus, Pogonias cromis, Archosargus probatocephalus) to be highest in low turbidity (< 30 nephelometric turbidity units [NTU]; p < 0.01), while crab (Callinectes sapidus) abundance was highest in high turbidity (> 30 NTU; p < 0.05). In field studies, mud crabs (Panopeus spp.), an important intermediate predator on oyster reefs that are not targeted in the 18 yr data set, were more abundant on oyster reefs in St. Charles Bay, Texas, when turbidity exceeded 30 NTU (p = 0.03). Fish predation on tethered Panopeus herbstii was greatest when turbidity was low (< 30 NTU, p < 0.05), but predation by crabs (p = 0.003) and overall predation (p = 0.02) were greatest in high turbidity (> 30 NTU). Predation on oyster spat was not different between low‐ and high‐turbidity sites (p = 0.64). However, oysters devoted more resources to shell growth (p < 0.01) at a cost of less somatic growth and fecundity, a reaction known to occur in response to crab predators. Elevated turbidity can alter trophic interactions in estuaries by altering species composition and trophic interactions, leading to an increase in crab abundance, which can alter predation rates as well as growth in juvenile oysters.

Proactive Restoration: Planning, Implementation, and Early Results of Silvicultural Strategies for Increasing Resilience against Gypsy Moth Infestation in Upland Oak Forests on the Daniel Boone National Forest, Kentucky

Determining targets in forest restoration is a complicated task that can be facilitated by cooperative partnerships. Too often restoration plans are implemented after adverse events that cause widespread tree mortality, such as drought or insect outbreaks, have occurred. Reactive management precludes the use of preemptive management techniques that can result in more effective restoration. The potential recognition and risks associated with a large-scale mortality event cultivated a proactive partnership among managers, stakeholders, and researchers on the Daniel Boone National Forest in Kentucky. This partnership resulted in the development of innovative proactive approaches to mitigate the negative impacts of threat of declining forest health, thus reducing the need for untested and expensive postdisturbance restorative operations. The partnership comprised four Research Work Units in the USDA Forest Service (including the Northern and Southern Research Stations), three universities (one land grant and two liberal arts), two natural resource state agencies, private logging contractors, an electrical utility, and National Forest system personnel at the district, forest supervisor, and Washington office levels. We tested forest management prescriptions designed to meet targets for future forest conditions. The goal of the silviculture treatments was to improve forest health and productivity to increase resilience to and/or avoidance of exotic invasive insect defoliation and oak decline. Treatments varied from high levels of disturbance to low levels of disturbance and ranged from even-aged regeneration treatments coupled with prescribed burning to thinning. Research assessed the alteration in species composition and stand structure, the projected regeneration outcomes and the costs and operational efficacy of mechanized forest operations used to implement the treatments. The relatively large scale of the study and diversity of treatments has afforded additional multidisciplinary research activities. Via partnership building and information and technology sharing, this project has been sustained for 10 years.

Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252).

The indigenous bacterial communities in sediment microcosms from Dauphin Island (DI), Petit Bois Island (PB) and Perdido Pass (PP) of the coastal Gulf of Mexico were compared following treatment with Macondo oil (MC252) using pyrosequencing and culture-based approaches. After quality-based trimming, 28,991 partial 16S rRNA sequence reads were analyzed by rarefaction, confirming that analyses of bacterial communities were saturated with respect to species diversity. Changes in the relative abundances of Proteobacteria, Bacteroidetes and Firmicutes played an important role in structuring bacterial communities in oil-treated sediments. Proteobacteria were dominant in oil-treated samples, whereas Firmicutes and Bacteroidetes were either the second or the third most abundant taxa. Tenericutes, members of which are known for oil biodegradation, were detected shortly after treatment, and continued to increase in DI and PP sediments. Multivariate statistical analyses (ADONIS) revealed significant dissimilarity of bacterial communities between oil-treated and untreated samples and among locations. In addition, a similarity percentage analysis showed the contribution of each species to the contrast between untreated and oil-treated samples. PCR amplification using DNA from pure cultures of Exiguobacterium, Pseudoalteromonas, Halomonas and Dyadobacter, isolated from oil-treated microcosm sediments, produced amplicons similar to polycyclic aromatic hydrocarbon-degrading genes. In the context of the 2010 Macondo blowout, the results from our study demonstrated that the indigenous bacterial communities in coastal Gulf of Mexico sediment microcosms responded to the MC252 oil with altered community structure and species composition. The rapid proliferation of hydrocarbonoclastic bacteria suggests their involvement in the degradation of the spilt oil in the Gulf of Mexico ecosystem.

Effects of topographic and edaphic conditions on alpine plant species distribution along a slope gradient on Mount Norikura, central Japan

AbstractThis study examined the effects of topographic and edaphic conditions on alpine plant species distribution along a slope gradient on Mt. Norikura (3026 m a.s.l.), central Japan. Topographic and edaphic factors investigated at 40 plots were: slope inclination, ground surface texture, soil water content and soil inorganic nitrogen concentration (NO3‐N, NH4‐N). The topographic and edaphic factors changed with slope positions: slope inclination was steeper, soil texture was coarser, and soil water and inorganic nitrogen concentration decreased with increasing slope position. Five vegetation types were located along the slope gradient and related to two factor‐groups: (1) changes in soil water, NH4‐N, slope inclination along the slope gradient, and (2) ground surface texture. A tall herbaceous plant community developed at the low slope position, near tarns, with fine soil surface texture, high soil water and NH4‐N, while Dicentra peregrina dominated on an unstable rubble slope near the ridge top. The distribution of each species was predictable from the two factor‐groups. Although the five vegetation types were related to the two factor‐groups, responses to the two factor‐groups differed among species, even within the same vegetation type. Therefore, this study showed that the topography of the terrain largely regulated alpine plant distribution by affecting edaphic conditions, and that global warming may alter species composition by changing edaphic conditions.

Can retention forestry help conserve biodiversity? A meta-analysis.

Industrial forestry typically leads to a simplified forest structure and altered species composition. Retention of trees at harvest was introduced about 25 years ago to mitigate negative impacts on biodiversity, mainly from clearcutting, and is now widely practiced in boreal and temperate regions. Despite numerous studies on response of flora and fauna to retention, no comprehensive review has summarized its effects on biodiversity in comparison to clearcuts as well as un-harvested forests. Using a systematic review protocol, we completed a meta-analysis of 78 studies including 944 comparisons of biodiversity between retention cuts and either clearcuts or un-harvested forests, with the main objective of assessing whether retention forestry helps, at least in the short term, to moderate the negative effects of clearcutting on flora and fauna. Retention cuts supported higher richness and a greater abundance of forest species than clearcuts as well as higher richness and abundance of open-habitat species than un-harvested forests. For all species taken together (i.e. forest species, open-habitat species, generalist species and unclassified species), richness was higher in retention cuts than in clearcuts. Retention cuts had negative impacts on some species compared to un-harvested forest, indicating that certain forest-interior species may not survive in retention cuts. Similarly, retention cuts were less suitable for some open-habitat species compared with clearcuts. Positive effects of retention cuts on richness of forest species increased with proportion of retained trees and time since harvest, but there were not enough data to analyse possible threshold effects, that is, levels at which effects on biodiversity diminish. Spatial arrangement of the trees (aggregated vs. dispersed) had no effect on either forest species or open-habitat species, although limited data may have hindered our capacity to identify responses. Results for different comparisons were largely consistent among taxonomic groups for forest and open-habitat species, respectively. Synthesis and applications. Our meta-analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention. Nevertheless, retention forestry will not substitute for conservation actions targeting certain highly specialized species associated with forest-interior or open-habitat conditions. Our meta-analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention. Nevertheless, retention forestry will not substitute for conservation actions targeting certain highly specialized species associated with forest-interior or open-habitat conditions.

Salvage logging affects early post-fire tree composition in Canadian boreal forest

Salvage logging following fire has become increasingly used during the last few decades as a way to mitigate economic losses caused by fire. The removal of burned mature trees including their aerial seedbanks immediately after fire could have impacts on post-fire tree recruitment but specific effects are still unknown. We conducted a study of a fire in the boreal forest of Québec, Canada, to answer the following questions: Does fire severity influence tree compositional changes after fire? Does salvage logging affect these changes by favouring species that can reproduce vegetatively? Does salvage logging reduce among-sites heterogeneity relative to natural post-fire forests? To address these questions, we measured pre- and post-fire tree stocking (2years after fire) of burned forest of different pre-fire stand composition types both in salvaged and non-salvaged sites, whereas fire severity was measured in the latter only. Species composition was evaluated using a Principal Component Analysis, and mixed models were used to test the effects of canopy fire severity, residual organic layer thickness, stand type and salvage logging on pre- to post-fire composition changes. In non-salvaged sites, fire severity had a significant effect on composition changes, and the effect depended on stand type. Low fire severity favoured species that can reproduce vegetatively such as Populus tremuloides, whereas moderate and high fire severity favoured the aerial seedbank species such as Pinus banksiana and Picea mariana. We found no effect of residual organic layer thickness on post-fire composition changes. Salvage treatment had a significant effect on post-fire composition changes and the effect depended on stand type. Overall, salvage logging tended to favour species relying upon vegetative reproduction more than fire alone, which favoured P. banksiana. Although among-site heterogeneity after salvage logging was not smaller than after fire only, salvage alters species composition more than does natural fire alone. Since salvage logging and low severity portions of the burn, which are generally not salvaged, both favour tree species with vegetative reproduction, our results suggest that these species will increase their dominance throughout the landscape if burned forests are systematically salvaged. We suggest strategies that can help to attenuate this divergence from natural post-fire conditions.

Epiphyte response to drought and experimental warming in an Andean cloud forest.

The high diversity and abundance of vascular epiphytes in tropical montane cloud forest is associated with frequent cloud immersion, which is thought to protect plants from drought stress. Increasing temperature and rising cloud bases associated with climate change may increase epiphyte drought stress, leading to species and biomass loss. We tested the hypothesis that warmer and drier conditions associated with a lifting cloud base will lead to increased mortality and/or decreased recruitment of epiphyte ramets, altering species composition in epiphyte mats. By using a reciprocal transplant design, where epiphyte mats were transplanted across an altitudinal gradient of increasing cloud immersion, we differentiated between the effects of warmer and drier conditions from the more general prediction of niche theory that transplanting epiphytes in any direction away from their home elevation should result in reduced performance. Effects differed among species, but effects were generally stronger and more negative for epiphytes in mats transplanted down slope from the highest elevation, into warmer and drier conditions, than for epiphyte mats transplanted from other elevations. In contrast, epiphytes from lower elevations showed greater resistance to drought in all treatments. Epiphyte community composition changed with elevation, but over the timescale of the experiment there were no consistent changes in species composition. Our results suggest some epiphytes may show resistance to climate change depending on the environmental and evolutionary context. In particular, sites where high rainfall makes cloud immersion less important for epiphyte water-balance, or where occasional drought has previously selected for drought-resistant taxa, may be less adversely affected by predicted climate changes.

Species and function lost: Role of drought in structuring stream communities

Drought is an important natural disturbance that influences community structure by altering species composition, abundance, and richness. Human-induced alterations of the hydrologic cycle and climate change can exacerbate the impact of drought, potentially leading to species extirpations and changes in community structure. These changes in community structure can lead to substantial alterations and losses of ecosystem functions. Nutrient recycling is an important ecosystem function that helps modify rates of production and food web structure. Animals are important in cycling and storing nutrients in aquatic ecosystems through feeding, growth, and excretion. Freshwater mussels are long-lived animals, often living more than 20years, and perform important ecosystem functions such as nutrient storage and cycling. Mussels dominate benthic biomass in many aquatic systems, and thus can be an essential component affecting nutrient dynamics. Unfortunately, they are experiencing rapid declines. In this study, we surveyed freshwater mussel populations across nine sites in three rivers in the south-central U.S. immediately before and after an exceptional, regional drought. We characterized the hydrological severity of the drought and estimated mussel biomass loss and the consequent loss of mussel-provided nutrient cycling and storage. We determined if losses differed between mussel thermal guilds and how such losses might influence nutrient dynamics and stoichiometry. Additionally, we investigated whether losses caused by the drought were intensified by different land cover types. Our surveys indicated that there were declines in both density and biomass of mussels, and greater losses were associated with areas that had less forest cover. This die-off resulted in a lower availability of N and reduced P storage by freshwater mussels in these rivers, potentially altering system nutrient availability. Additionally, our analyses showed that thermally sensitive species have lower tissue N:P. Thus, our results show that differences in species tolerance to drought may lead to varying storage and release of nutrients. Further studies incorporating net flux and storage will allow scientists to better understand the repercussions of species loss to ecosystem function.

Epiphyte response to drought and experimental warming in an Andean cloud forest

The high diversity and abundance of vascular epiphytes in tropical montane cloud forest is associated with frequent cloud immersion, which is thought to protect plants from drought stress. Increasing temperature and rising cloud bases associated with climate change may increase epiphyte drought stress, leading to species and biomass loss. We tested the hypothesis that warmer and drier conditions associated with a lifting cloud base will lead to increased mortality and/or decreased recruitment of epiphyte ramets, altering species composition in epiphyte mats. By using a reciprocal transplant design, where epiphyte mats were transplanted across an altitudinal gradient of increasing cloud immersion, we differentiated between the effects of warmer and drier conditions from the more general prediction of niche theory that transplanting epiphytes in any direction away from their home elevation should result in reduced performance. Effects differed among species, but effects were generally stronger and more negative for epiphytes in mats transplanted down slope from the highest elevation, into warmer and drier conditions, than for epiphyte mats transplanted from other elevations. In contrast, epiphytes from lower elevations showed greater resistance to drought in all treatments. Epiphyte community composition changed with elevation, but over the timescale of the experiment there were no consistent changes in species composition. Our results suggest some epiphytes may show resistance to climate change depending on the environmental and evolutionary context. In particular, sites where high rainfall makes cloud immersion less important for epiphyte water-balance, or where occasional drought has previously selected for drought-resistant taxa, may be less adversely affected by predicted climate changes.

Grazing depletes forb species diversity in the mesic grasslands of KwaZulu-Natal, South Africa

Forbs constitute over 80% of the species richness of mesic grassland but their response to grazing is largely unknown. The influence of grazing on the forb composition, richness and diversity of two species-rich grasslands in the coastal hinterland and midlands of KwaZulu-Natal, South Africa was examined in plots subject to grazing intensities ranging from lightly grazed nature reserves through to heavily stocked communal areas and commercial ranches. Grazing altered forb species composition and considerably reduced forb richness and Shannon diversity in both grasslands. Mean forb richness declined by 64–84%, from 50–55 species per 100 m2 in lightly grazed areas to fewer than 10–20 species in the most heavily grazed plots. Many long-lived perennial indigenous forbs were extirpated or markedly reduced in abundance by overgrazing and replaced by a few, mostly exotic, hardy species, suggesting these grasslands did not evolve under heavy grazing. Indigenous forb richness was non-linearly related to, and thus not reliably predicted by, range condition score and the abundance of two dominant decreaser and increaser grasses, but the poorest grassland was the most depauperate and good condition grassland was invariably diverse. Judicious grazing management with light stocking is thus required to maintain the diversity of mesic grassland.

Increased prevalence and altered species composition of filamentous fungi in respiratory specimens from cystic fibrosis patients

Filamentous fungi cultured from respiratory tract specimens submitted to the department of clinical microbiology, Aarhus University Hospital, during 2010 were identified by morphology and by internal transcribed spacer (ITS) sequencing. Of 343 fungal isolates, discrepancies between identification methods were observed for four isolates (1.2%), while identification to species was achieved only with ITS sequencing for 16 isolates (4.7%). Filamentous fungi were isolated from 15% of cystic fibrosis (CF) respiratory samples in contrast to 2% of non-CF samples. From CF patients, a total of nine different species were found in 188 samples from 48 patients, whereas from non-CF patients, 24 different species were found in 155 samples from 111 patients. CF was associated with a significant overrepresentation of Aspergillus fumigatus and Scedosporium species; in contrast, the frequency of Penicillium spp. and other putative contaminants were significantly increased in non-CF patients. The altered species variation of filamentous fungi in CF respiratory specimens is contradictory to a scenario of incidentally inhaled spores, trapped in the viscous airway mucus of these patients and subsequently expectorated; rather, our data most likely reflect both an increased prevalence and an increased proportion of truly colonizing fungi in this patient group.

Seabird nutrient subsidies benefit non-nitrogen fixing trees and alter species composition in South American coastal dry forests.

Marine-derived nutrients can increase primary productivity and change species composition of terrestrial plant communities in coastal and riverine ecosystems. We hypothesized that sea nutrient subsidies have a positive effect on nitrogen assimilation and seedling survival of non-nitrogen fixing species, increasing the relative abundance of non-nitrogen fixing species close to seashore. Moreover, we proposed that herbivores can alter the effects of nutrient supplementation by preferentially feeding on high nutrient plants. We studied the effects of nutrient fertilization by seabird guano on tree recruitment and how these effects can be modulated by herbivorous lizards in the coastal dry forests of northwestern Peru. We combined field studies, experiments and stable isotope analysis to study the response of the two most common tree species in these forests, the nitrogen-fixing Prosopis pallida and the non-nitrogen-fixing Capparis scabrida. We did not find differences in herbivore pressure along the sea-inland gradient. We found that the non-nitrogen fixing C. scabrida assimilates marine-derived nitrogen and is more abundant than P. pallida closer to guano-rich soil. We conclude that the input of marine-derived nitrogen through guano deposited by seabirds feeding in the Pacific Ocean affects the two dominant tree species of the coastal dry forests of northern Peru in contrasting ways. The non-nitrogen fixing species, C. scabrida may benefit from sea nutrient subsidies by incorporating guano-derived nitrogen into its foliar tissues, whereas P. pallida, capable of atmospheric fixation, does not.

Epiphyte response to drought and experimental warming

The high diversity and abundance of vascular epiphytes in tropical montane cloud forest is associated with frequent cloud immersion, which is thought to protect plants from drought stress. Increasing temperature and rising cloud bases associated with climate change may increase epiphyte drought stress, leading to species and biomass loss. We tested the hypothesis that warmer and drier conditions associated with a lifting cloud base will lead to increased mortality and/or decreased recruitment of epiphyte ramets, altering species composition in epiphyte mats. By using a reciprocal transplant design, where epiphyte mats were transplanted across an altitudinal gradient of increasing cloud immersion, we differentiated between the effects of warmer and drier conditions from the more general prediction of niche theory that transplanting epiphytes in any direction away from their home elevation should result in reduced performance. Ramet mortality increased, recruitment decreased, and population size declined for epiphytes in mats transplanted down slope from the highest elevation, into warmer and drier conditions, but epiphytes from lower elevations showed greater resistance to drought in all treatments. Epiphyte community composition changed with elevation, but over the timescale of the experiment there were no consistent changes in species composition. Our results suggest some epiphytes may show resistance to climate change depending on the environmental context, although if climate change results in consistently drier conditions and higher cloud bases, biomass loss and shifting species composition in epiphyte communities is likely.

Novel ecosystems in the Anthropocene: a revision of the novel ecosystem concept for pragmatic applications

Ecologists have developed terminology to distinguish ecosystems based on the degree of human alteration. To this end, ecosystems can be characterized as ecosystems, impacted ecosystems, or ecosystems, depending on the role of human management in development and effects on properties. Properly classifying an as novel, impacted, or designed has critical implications for its conservation and management, but a broadly applicable definition for a ecosystem does not exist. We have provided a formal definition of ecosystem that facilitates its use in practical applications and have described four characteristics of such an ecosystem. A novel can be identified by its origins rooted in human agency, the ecological thresholds it has crossed, a significantly altered species composition, and a capacity to sustain itself. Ecosystem classification in the literature has been inconsistent. We have illustrated the application of our definition using multiple case studies representing impacted, designed, and novel ecosystems.

Post-fire salvage logging alters species composition and reduces cover, richness, and diversity in Mediterranean plant communities

An intense debate exists on the effects of post-fire salvage logging on plant community regeneration, but scant data are available derived from experimental studies. We analyzed the effects of salvage logging on plant community regeneration in terms of species richness, diversity, cover, and composition by experimentally managing a burnt forest on a Mediterranean mountain (Sierra Nevada, S Spain). In each of three plots located at different elevations, three replicates of three treatments were implemented seven months after the fire, differing in the degree of intervention: “Non-Intervention” (all trees left standing), “Partial Cut plus Lopping” (felling 90% of the trees, cutting the main branches, and leaving all the biomass in situ), and “Salvage Logging” (felling and piling the logs, and masticating the woody debris). Plant composition in each treatment was monitored two years after the fire in linear point transects. Post-fire salvage logging was associated with reduced species richness, Shannon diversity, and total plant cover. Moreover, salvaged sites hosted different species assemblages and 25% lower cover of seeder species (but equal cover of resprouters) compared to the other treatments. Cover of trees and shrubs was also lowest in Salvage Logging, which could suggest a potential slow-down of forest regeneration. Most of these results were consistent among the three plots despite plots hosting different plant communities. Concluding, our study suggests that salvage logging may reduce species richness and diversity, as well as the recruitment of woody species, which could delay the natural regeneration of the ecosystem.

Ecology of Native vs. Introduced Phragmites australis (Common Reed) in Chicago-Area Wetlands

Rapid spread of Phragmites australis (common reed) in North American wetlands is widely attributed to cryptic invasion by an introduced lineage. However, in the Midwestern U.S., the native subspecies (subsp. americanus) may also exhibit rapid expansion. Where both lineages occur, wetland managers are sometimes unsure whether they should limit management activities to the introduced lineage or control both. We conducted field studies to contrast the ecology of native and introduced Phragmites by pairing patches of each with native reference vegetation. We measured each lineage’s association with environmental conditions, their growth metrics (stem heights, stem densities, and plant cover), and their invasiveness as indicated by the diversity and composition of associated plant communities. Introduced Phragmites exhibited more robust growth than the native, and its growth was more positively correlated with increases in soil nutrient availability and salinity. Areas with introduced Phragmites had lower plant diversity and altered species composition relative to reference vegetation. We did not observe similar evidence of invasiveness in native Phragmites. We encourage wetland managers to differentiate populations by lineage and, unless there is compelling evidence to do otherwise, restrict control efforts to the introduced lineage.

Metaproteomics to unravel major microbial players in leaf litter and soil environments:Challenges and perspectives

Soil- and litter-borne microorganisms vitally contribute to biogeochemical cycles. However, changes in environmental parameters but also human interferences may alter species composition and elicit alterations in microbial activities. Soil and litter metaproteomics, implying the assignment of soil and litter proteins to specific phylogenetic and functional groups, has a great potential to provide essential new insights into the impact of microbial diversity on soil ecosystem functioning. This article will illuminate challenges and perspectives of current soil and litter metaproteomics research, starting with an introduction to an appropriate experimental design and state-of-the-art proteomics methodologies. This will be followed by a summary of important studies aimed at (i) the discovery of the major biotic drivers of leaf litter decomposition, (ii) metaproteomics analyses of rhizosphere-inhabiting microbes, and (iii) global approaches to study bioremediation processes. The review will be closed by a brief outlook on future developments and some concluding remarks, which should assist the reader to develop successful concepts for soil and litter metaproteomics studies.