Important Ecological Functions Research Articles

Farmland Birds and their Importance in Agro ecosystem: A Review

Avian fauna provide a variety of functions, including predators, pollinators, scavengers, seed dispersers, pests controller, nutrient cycling, ecosystem engineers, and many others. Birds play important ecological and economic functions however they are sometimes overlooked simply because of a lack of knowledge. However, as bird populations drop globally, so do the ecological advantages given by these species. To support bird conservation, this review study focuses on the role of birds in the agro-ecosystem and their benefits to humans. Biodiversity databases and existing literature were reviewed to establish baseline information on farmland bird species and their preferences. Searches were limited to articles published between 2005 to 2024. Healthy bird populations and habitats would help to safeguard a variety of ecological functions, ultimately benefiting human health. Farmland birds are disappearing. Due to the widespread use of pesticides, lack of habitat, birds and other animals are disappearing and unnecessary harmful pest species are increasing and the agricultural environment is deteriorating. So, this review paper tries to emphasize on urgent conservation measures that are necessary for the protection of agricultural birds which are essential for the health of both natural and agricultural environments.

Assessment of agroclimatic resources in agricultural landscapes of the Turkestan region of the Republic of Kazakhstan Askha

The article presents the scientific results of a study assessing agroclimatic resources in agricultural landscapes located in various natural zones of the Turkestan region of the RK (Republic of Kazakhstan). The research methods included classical and modern methods of mathematical statistics using digital technology and time series graphs to develop a mathematical model for climatic and hydrological indicators. Assessment of changes in indicators of agroclimatic resources in agricultural landscapes for 1941–2020 showed that the sum of air temperature, evaporation from the water surface and radiation balance of the daytime surface, characterising the energy resources of landscapes, increased by 10–15%, which contributes to increase in the total water consumption of agricultural land by 10–12%. Meanwhile, the decreasing tendency of the amount of precipitation by 5–10% in all natural climatic zones of the region has become one of the factors leading to a decrease in the natural moisture supply of the soil and vegetation cover of landscapes by 10–15%, acting as important environment-forming and ecological functions. The combined impact of these environment-forming factors has become the key reason for the increase in the deficit of agricultural land water consumption by 15–20%, the reduction of solar energy costs for the soil-forming process by 10–15% and the increase of the climate aridisation, and has become a signal for the need in the safety of agricultural activities, requiring the development of a set of adaptive measures to mitigate this process in the region.

Drag coefficients and water surface profiles in channels with arrays of linear rigid emergent vegetation

Although vegetation in watercourses has an important ecological function, from a hydraulic point of view, it increases flow resistance, determinates higher water levels and generates a greater risk of flooding. In engineering practice, to determine water levels, the drag coefficient must be known, whose experimental values, in literature, are provided for uniform or quasi-uniform flow. In this paper, the expression of a drag coefficient, previously proposed by the authors for the case of emergent rigid vegetation arranged in a linear manner, was used to simulate experimental water surface profiles, employing the effective width for the first time. The formula was validated by simulating 26 experimental profiles observed at the University of Calabria, over 1100 points in total, plus 8 published in literature. In some of these applications, the vegetation density was much higher than that for which the drag coefficient expression was derived. For this reason, it is possible to consider a new, wider field of validity for it. The proposed equation is independent of the Reynolds stem number, so that it can be used in natural streams and rivers, provided that viscosity effects can be considered negligible. Finally, some comments are offered on the application of a new formula proposed in literature regarding the computation of the profile when downstream depth is taken as a boundary condition.

Groundwaterscapes: A Global Classification and Mapping of Groundwater's Large‐Scale Socioeconomic, Ecological, and Earth System Functions

AbstractGroundwater is a dynamic component of the global water cycle with important social, economic, ecological, and Earth system functions. We present a new global classification and mapping of groundwater systems, which we call groundwaterscapes, that represent predominant configurations of large‐scale groundwater system functions. We identify and map 15 groundwaterscapes which offer a new lens to conceptualize, study, model, and manage groundwater. Groundwaterscapes are derived using a novel application of sequenced self‐organizing maps that capture patterns in groundwater system functions at the grid cell level (∼10 km), including groundwater‐dependent ecosystem type and density, storage capacity, irrigation, safe drinking water access, and national governance. All large aquifer systems of the world are characterized by multiple groundwaterscapes, highlighting the pitfalls of treating these groundwater bodies as lumped systems in global assessments. We evaluate the distribution of Global Groundwater Monitoring Network wells across groundwaterscapes and find that industrial agricultural regions are disproportionately monitored, while several groundwaterscapes have next to no monitoring wells. This disparity undermines the ability to understand system dynamics across the full range of settings that characterize groundwater systems globally. We argue that groundwaterscapes offer a conceptual and spatial tool to guide model development, hypothesis testing, and future data collection initiatives to better understand groundwater's embeddedness within social‐ecological systems at the global scale.

Overcoming challenges to access ecological function: a marine soft-bottom perspective

Ecosystem functioning studies have gained prominence due to concerns about the decline of species. In marine sediments, benthic invertebrates perform important ecological functions. However, the challenges within the field of functional ecology are sparsely discussed. Our aim was to systematize the problems and suggest pathways forward. To achieve this, we review recent articles on functional ecology on marine sediments and identified two main issues. First, the absence of a clear definition of terms. Second, in terms of applicability, we observed a mismatch between the scales of functioning and traits, incomplete information on trait databases, inappropriate selection of traits, subjective measures of traits, overlooked trait variability and data analyses without the link between the taxonomy and the traits associated with functions. We propose some pathways to overcome the challenges, such as (i) reasoning of the concept of function, process and trait, (ii) increasing experiments to measure functions, (iii) clarification of the relationship between traits and functions, (iv) clear procedure for assigning trait scores, (v) experiments for understanding trait variability and function performance, and (vi) analyses that consider the sets of traits of each taxon. Overcoming these challenges will allow us to advance research and fill gaps in knowledge of ecosystem functioning.

Bee–plant interactions identified by pollen analysis of honey from the stingless bee Tetragonisca fiebrigi (Schwarz, 1938) in southern Brazil

ABSTRACT Pollen analysis of honey reveals information about bee–plant interactions and networks that, in some cases, are lost through mere observation of bees on flowers. This information on bee–plant interactions is valuable for the protection of bees and vegetal speciesand pollination of crop plants. To provideinsights into bee–plant interactions, palynological evidence was developedfromthe collection of honey. The objective of this study is to determine the plants that the bees (Tetragonisca fiebrigi) visit for honey production in southern Brazil (Rio Grande do Sul). For this, 24 honey samples were collectedfrom five regions of northeastern Rio Grande do Sul, southern Brazil. A total of 64 pollen types were found in the honey samples fromT.fiebrigi in southern Brazil, mainly from trees. The most common pollen types in the samples were from Schinus terebinthifolia, Schizolobium parahyba, Handroanthus sp., Morus nigra, and Rosa cf. grandiflora. The pollen grains show a high diversity of plants, including those with important ecological functions.

Assembly and maintenance of phyllosphere microbial diversity during rubber tree leaf senescence

Phyllosphere microorganisms execute important ecological functions including supporting host plant growth, enhancing host resistance to abiotic stresses, and promoting plant diversity. How leaf developmental stages affect plant-microbiome interactions and phyllosphere microbial community assembly and diversity is poorly understood. In this study, we utilized amplicon sequencing of 16S rRNA and ITS genes to investigate the composition and diversity of microbial communities across different leaf developmental stages of rubber trees. Our findings reveal that endophytic microbial communities, particularly bacterial communities, are more influenced by leaf senescence than by epiphytic communities. The high abundance of metabolism genes in the endosphere of yellow leaves contributes to the degradation and nutrient relocation processes. Nutrient loss leads to a higher abundance of α-Proteobacteria (r-selected microorganisms) in the yellow leaf endosphere, thereby promoting stochastic community assembly. As leaves age, the proportion of microorganisms entering the inner layer of leaves increases, consequently enhancing the diversity of microorganisms in the inner layer of leaves. These results offer insights into the mechanisms governing community assembly and diversity of leaf bacteria and fungi, thereby advancing our understanding of the evolving functions of microbial communities during leaf senescence in general, and for an important tropical crop species in particular.

Spatiotemporal evolution and driving mechanism of Dongting Lake based on 2005–2020 multi-source remote sensing data

As one of the largest inland lakes in China, Dongting Lake has attracted widespread attention owing to its rich natural resources, unique geographical landscape, and important ecological functions. Recently, Dongting Lake has experienced phenomena such as an early dry season and backflow during the flood season. Multi-source remote sensing data and the normalised difference water index (NDWI) threshold method were used to systematically analyse the water area of the lake from 2005 to 2020. Additionally, it employed a centre of gravity migration model and a geographic detector model to investigate the lake's evolution patterns and driving mechanisms. The research identified notable fluctuations in Dongting Lake's water area during this period, with a particularly sharp decline in 2006—from 1509.74 km2 to 815 km2, marking a decrease of 694.74 km2 and a shrinkage rate of 46.01 %. Spatial analysis indicated that the centre of gravity of these water areas changed primarily between Nandashan Town, the Dongting Lake Management Committee, Wanzihu Township, and Qingtan Township, underscoring their significant influence on lake dynamics, including runoff, surface water availability, sediment deposition, and precipitation, all of which displayed strong positive correlations (Pearson coefficients of 0.57, 0.68, and 0.63, respectively), whereas population density showed a negative correlation (Pearson coefficient of −0.56). Furthermore, the study highlighted the substantial impact of the Digital Elevation Model (DEM) and its interaction with slope and aspect on Dongting Lake's evolution, with Q values of 0.537 and 0.543, respectively, emphasising their critical roles in shaping lake area changes and providing a crucial scientific basis for enhancing the understanding and effective management of water resources in the Dongting Lake Basin through comprehensive analysis of its spatiotemporal evolution and driving mechanisms.

Spatio-temporal Dynamics of Land Use/Cover Change and Associated Carbon Stocks in Kanyabaha Wetland in Rukiga District, Uganda

Wetlands play an important ecological function of sequestering atmospheric carbon dioxide and thereby moderating adverse impacts of climate change. It is therefore important to understand the dynamics of carbon stocks in wetland vegetation and soils. This study investigated the spatio-temporal dynamics of aboveground, belowground, and total carbon stocks in Kanyabaha Wetland, located in Rukiga District, Uganda, spanning from 1990 to 2021. Through field sampling and laboratory analysis, aboveground carbon stocks were assessed by harvesting vegetation biomass and converting it to carbon stock using established conversion factors. Soil samples collected at different depths (0-20cm, 20-50cm, 50-100cm) were analyzed for soil organic carbon content to determine belowground carbon stocks. The study reveals variable spatio-temporal patterns of carbon stocks across land use types, with papyrus-dominated areas exhibiting the highest aboveground carbon stocks (49.66 tC/ha), followed by small-scale farmlands (33.73 tC/ha) and tree plantations (23.01 tC/ha). Conversely, built-up areas exhibit the lowest carbon stocks (1.29 tC/ha). Temporal analysis reveals fluctuating patterns in carbon stocks, with increases observed in built-up areas and small-scale farmlands, and decreases in grasslands and tree plantations that could be due to changes in hydrological cycle. Belowground carbon stocks follow similar trends, with papyrus areas maintaining the highest stocks (39.96 tC/ha), particularly at deeper soil depths that exhibit the highest carbon accumulation due to its extensive network of papyrus rhizome. Changes in land use, especially reclamation of the wetlands for farming and settlements affected carbon capture and storage in the wetland ecosystem. These findings highlight the importance of targeted conservation of natural wetlands and sustainable land management strategies in the Kanyabaha Wetland catchment for enhanced carbon sequestration. Further, in depth studies in the variability of carbon stocks due to various eco-climatic factors and anthropogenic activities are necessary to support sustainable wetland land management practices in Uganda.

RAIChU: automating the visualisation of natural product biosynthesis

Natural products are molecules that fulfil a range of important ecological functions. Many natural products have been exploited for pharmaceutical and agricultural applications. In contrast to many other specialised metabolites, the products of modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) systems can often (partially) be predicted from the DNA sequence of the biosynthetic gene clusters. This is because the biosynthetic pathways of NRPS and PKS systems adhere to consistent rulesets. These universal biosynthetic rules can be leveraged to generate biosynthetic models of biosynthetic pathways. While these principles have been largely deciphered, software that leverages these rules to automatically generate visualisations of biosynthetic models has not yet been developed. To enable high-quality automated visualisations of natural product biosynthetic pathways, we developed RAIChU (Reaction Analysis through Illustrating Chemical Units), which produces depictions of biosynthetic transformations of PKS, NRPS, and hybrid PKS/NRPS systems from predicted or experimentally verified module architectures and domain substrate specificities. RAIChU also boasts a library of functions to perform and visualise reactions and pathways whose specifics (e.g., regioselectivity, stereoselectivity) are still difficult to predict, including terpenes, ribosomally synthesised and posttranslationally modified peptides and alkaloids. Additionally, RAIChU includes 34 prevalent tailoring reactions to enable the visualisation of biosynthetic pathways of fully maturated natural products. RAIChU can be integrated into Python pipelines, allowing users to upload and edit results from antiSMASH, a widely used BGC detection and annotation tool, or to build biosynthetic PKS/NRPS systems from scratch. RAIChU’s cluster drawing correctness (100%) and drawing readability (97.66%) were validated on 5000 randomly generated PKS/NRPS systems, and on the MIBiG database. The automated visualisation of these pathways accelerates the generation of biosynthetic models, facilitates the analysis of large (meta-) genomic datasets and reduces human error. RAIChU is available at https://github.com/BTheDragonMaster/RAIChU and https://pypi.org/project/raichu.Scientific contributionRAIChU is the first software package capable of automating high-quality visualisations of natural product biosynthetic pathways. By leveraging universal biosynthetic rules, RAIChU enables the depiction of complex biosynthetic transformations for PKS, NRPS, ribosomally synthesised and posttranslationally modified peptide (RiPP), terpene and alkaloid systems, enhancing predictive and analytical capabilities. This innovation not only streamlines the creation of biosynthetic models, making the analysis of large genomic datasets more efficient and accurate, but also bridges a crucial gap in predicting and visualising the complexities of natural product biosynthesis.

Attributing spatially stratified heterogeneity in biodiversity of urban–rural interlaced zones based on the OPGD model

Urban–rural interlaced zones are characterized by the interpenetration of urban and rural elements, drastic changes in construction, relatively weak planning and management, and anthropogenic activities that constantly impact the ecological background. However, the ecological barriers and hinterland spaces of the city center provide important ecological functions. In this study, we selected forest birds as indicator species of the urban ecological environment and explored the spatial stratification and heterogeneity effects of environmental substrates and anthropogenic activities on bird diversity (species richness, abundance, Shannon–Wiener index, and Simpson index) in urban–rural interlaced zones using the optimal parameter geographic detector model to characterize the changes in ecological functions in these zones. The results of this study are as follows:(1) The bird diversity index in Minhang District, Shanghai, showed an obvious urban-rural gradient divergence with the transition of urban zone- rural-urban interface - rural zone.An agglomerative spatial differentiation pattern was observed more in the southeast but less in the northwest, with a high degree of spatial distribution concentrations and evident imbalance characteristics.(2) The spatially stratified heterogeneity in bird diversity in urban–rural interlaced zones was because of the combined action of multiple driving factors under the three dimensions of habitat environment, degree of urbanization, and anthropogenic interference. Most of the interactions between any two factors showed non-linear or bifactorial enhancement effects. Furthermore, the one-factor explanatory power of urbanization and anthropogenic interference factors on bird diversity was significantly higher than that of the habitat environment factor.(3) Population heat distribution (PD), distance to the center of Shanghai (DC), and nighttime lighting index(NTL) were the main drivers of spatially stratified heterogeneity in bird diversity and the key indicators of urban–rural gradient changes. The interaction between PD and DC had the strongest explanatory power for the spatial differentiation of bird diversity.

PHYTOSOCIOLOGICAL CHARACTERIZATION OF AN URBAN FRAGMENT OF INTERIOR ATLANTIC FOREST - PARANÁ, BRAZIL

The Parque Natural Municipal Paulo Gorski, located in western Paraná, comprises an urban remnant of Mixed Ombrophilous Forest. This study aimed to identify tree species and conduct the phytosociological characterization of this fragment of the Atlantic Forest. Monthly visits were made in ten plots (20 x 5 m) to collect fertile samples. A rarefaction curve was generated, and phytosociological parameters, diversity, and the distribution of individuals in diameter classes were calculated. A total of 158 tree individuals were sampled, distributed across 23 families and 47 species (including six exotic ones). Among the species found, 74.4% exhibited zoochoric dispersion syndrome, 19.1% anemochoric, and 6.5% autocoric. Concerning successional category, 63.8% were early successional species. Alchornea triplinervia (Spreng.) Müll.Arg. and Prunus myrtifolia (L.) Urb. had the highest importance values due to their high number of individuals, greater frequency, and basal area. Araucaria angustifolia (Bertol.) Kuntz, an endangered species, also had a high importance value. The Shannon diversity index was 3.43, and evenness was 0.89. Approximately 70% of the individuals were distributed in smaller diameter classes (< 15 cm), forming an inverted J-shape, an expected pattern indicating a regenerative capacity and structure of preserved forest remnants, despite being in an urban area and facing significant human pressures. This urban forest fragment should be preserved, as it contains native and endangered tree species from the region, serving as an ecological corridor, and maintains important ecological and social functions for the region.

Community Structure of Sea Cucumbers (Holothuroidea) in The Intertidal Zone of Koepisino Beach, North Buton

Sea cucumbers are marine invertebrates belonging to the class Holothuroidea, living in various aquatic environments ranging from shallow coastal waters to deep seas. Sea cucumbers have an important ecological function in coral reef ecosystems. The aim of the research is to determine the community structure of sea cucumbers (Holothuroidea) in the intertidal zone of Koepisino Beach, North Buton. The research method used was quantitative descriptive research conducted in the intertidal zone of North Koepisino Buton Beach. Data collection was carried out by exploring each station measuring 50 × 100 meters for 3 stations. Data analysis was descriptive quantitative, In the intertidal zone of Koepisino Beach, North Buton, 12 species of sea cucumbers belonging to two orders, Aspidochirotida (genera Holothuria, Bohadschia, Telonata, and Stichopus) and Apodida (genera Synapta and Opheodesoma), were discovered. The community structure components analyzed in this study were abundance, diversity index, uniformity index, and dominance index.The highest abundance of sea cucumber species was at station I (sand substrate) at 0.009 (ind/m2). The lowest species abundance was at station III (coral rubble substrate) at 0.005 (ind/m2). H. scabra is the species with the highest abundance, namely 0.0026 ind/m2, while Bohadschia similis, Bohadschia vitiensis, Opheodesoma spectabilis, Telonata ananas are the species with the lowest abundance, namely 0 ind/m2. The Shannon-Wiener sea cucumber diversity index (H') is in the medium category 2.144. The sea cucumber uniformity index at the research location is high (E > 0.6) and there is no dominant species.

The Role of Organic Matter in Phosphorus Retention in Eutrophic and Dystrophic Terrestrial Ecosystems

Phosphorus (P) retention in soils in the presence of organic matter (OM) has been, for years, a topic with no clear conclusions. Considering the important ecological functions of peatlands, the objective of this study is to examine the role of OM transformation in relation to P status in Histosols in the Oder Valley (Poland). Basic physical and chemical properties and the following P forms were determined in the organic horizons of 5 soil profiles from two habitats (eutrophic and dystrophic): total (Pt) and organic P (Po), available P (PM3), easily soluble P (PCaCl2), water-soluble P (PW), and fraction of Po in humic (Po_HA) and fulvic (Po_FA) acids after extraction with 0.5 mol L−1 NaOH. The results were statistically verified in both examined habitat groups separately. The higher values of mobile P forms were found in the upper organic horizons released from OM constituents as a result of their decomposition. The role of OM in P retention was strongly related to the activity of humic substances (HS): a higher Po percentage (6.9–99.4% of Po) was observed in dystrophic, whereas a lower (9.3–28.6% of Po) was observed in eutrophic Histosols. Humic acids played a dominant role in P retention compared to fulvic acids in most peat horizons, especially at pH < 5. The role of HA and FA in P retention was clearly dependent on forms found only in eutrophic Histosols. The important role of FA in P retention during OM transformation was confirmed by negative correlations between Po_FA and macronutrient ratios in both soil groups. The results confirm the variable role of OM in P retention, depending on soil environmental conditions and OM type (peat and moorsh). This may have important applications not only in areas of natural importance, for which the release of mobile P forms may be a threat, but also in agricultural areas where, for a change, we struggle to increase P availability.

Razor clam (Pinna bicolor) structural mimics as drivers of epibenthic biodiversity; a manipulative experiment

Shellfish ecosystems facilitate important ecological functions and communities, but overexploitation and mismanagement have contributed to their decline worldwide. Within recent decades, coastal management efforts have increasingly sought to understand and reinstate valuable ecological functions provided by habitat-forming bivalves including oysters, mussels and pinnids. However, many bivalve species are critically understudied, limiting restoration and ecological engineering opportunities. Pinnids, specifically, are an underappreciated bivalve group, with razor clams (Pinna bicolor) forming dense aggregations, and potentially supporting important ecological functions. This study, conducted in an urban Australian estuary, was a manipulative experiment that investigated whether artificial razor clam shells could facilitate beneficial ecological functions through the provision of structural habitat. Specifically, we investigated the influence of intertidal benthic structures, including the micro-habitat influences of surface structure associated with mortality status (open or closed shell), and the short-term response of the benthic and epifaunal communities. Within 12 weeks, the structural razor clam mimics rapidly changed the aboveground ecological community, relative to the bare habitat controls. Both open and closed artificial shells provided a settlement surface for epiphytic organisms and supported enhanced epifaunal biodiversity. Contrastingly, the artificial structures did not significantly alter sediment characteristics or infaunal macroinvertebrate composition in the surrounding benthos. These results provide important insights into the rapid ecological response to the installation of intertidal pinnid structures in dynamic estuarine ecosystems. Furthermore, we provide a case study for understanding the ecological functions of an understudied habitat-forming species, which could be used to inform future restoration and management efforts.

Legacy and alternative perfluoroalkyl acids in the Yellow River on the Qinghai-Tibet Plateau: Levels, spatiotemporal characteristics, and multimedia transport processes

The source region of the Yellow River (SRYR) located in the northeast of the Qinghai-Tibetan Plateau is not only the largest runoff-producing area in the Yellow River Basin, but also the most important freshwater-supply ecological function area in China. In this study, the short-term spatiotemporal distribution of selected legacy and alternative perfluoroalkyl acids (PFAAs) in the SRYR was first investigated in multiple environmental media. Total PFAA concentrations were in the range of 1.16-14.3 ng/L, 4.25-42.1 pg/L, and 0.21-13.0 pg/g dw in rainwater, surface water, and sediment, respectively. C4-C7 PFAAs were predominant in various environmental matrices. Spatiotemporal characteristics were observed in the concentrations and composition profiles. Particularly, the spatial distribution of rainwater and the temporal distribution of surface water exhibited highly significant differences (p<0.01). Indian monsoon, westerly air masses, and local mountain-valley breeze were the driving factors that contributed to the change of rainwater. Rainwater, meltwater runoff, and precursor degradation were important sources of PFAA pollution in surface water. Organic carbon content was a major factor influencing PFAA distribution in sediment. These results provide a theoretical basis for revealing the regional transport and fate of PFAAs, and are also important prerequisites for effectively protecting the freshwater resource and aquatic environment of the Qinghai-Tibetan Plateau.

Soil fungal communities associated with chili pepper respond to mineral and organic fertilization and application of the biocontrol fungus Trichoderma harzianum

Soil fungi are diverse and common in crop systems with important ecological function such as saprotrophs, symbionts, and pathogens, all of which are key components for soil fertility and health. Agricultural practices including tillage, crop rotation, fertilization and pest management with pesticides and microbial biocontrol agents are known to affect the abundance and composition of soil fungi, but these factors are seldom integrated and studied in combination. The objective of this study was to examine the influence of mineral and organic (compost) fertilization, and soil inoculation with the biocontrol fungus Trichoderma harzianum individually and in combination on the resident soil fungal communities and plant performance in a greenhouse pot experiment with chili pepper grown in a disease-infested agricultural soil. Soil fungal communities were studied using Illumina MiSeq sequencing and taxonomic assignment using the UNITE database in terms of amplicon sequence variants (ASV). Main results showed that the combination of compost and T. harzianum inoculation completely controlled chili pepper wilt, which coincided with alterations in soil fungal diversity. The root pathogen Fusarium equiseti was the most abundant fungus (in relative terms) in all treatments and the ASV Trichoderma sp. was only found in the treatments in which T. harzianum had been applied. Soil application with T. harzianum at sowing also reduced chili pepper damping-off in non-sterile disease-infested soil, which coincided with a reduction of the relative abundance of F. equiseti. However, several other known Fusarium spp. pathogens were present in the natural disease infested agricultural soil and could also have been involved in the chili pepper wilt observed. In conclusion, our results show promising biocontrol traits of T. harzianum against chili pepper damping off and wilt most likely caused by Fusarium spp. The observed alterations in soil fungal diversity with T. harzianum and compost were probably involved in the reduction of chili pepper wilt but needs to be further studied.

Multi-biomarker approach reveals the effects of heavy metal bioaccumulation in the foundation species Prosopis laevigata (Fabaceae).

Mining is a major economic activity in many developing countries. However, it disturbs the environment, producing enormous quantities of waste, known as mine tailings, which can have deleterious environmental impact, due to their high heavy metals (HM) content. Often, foundation species that establish on mine tailings are good candidates to study the effects of HM bioaccumulation at different levels of biological organization. Prosopis laevigata is considered a HM hyperaccumulator which presents attributes of a foundation species (FS) and establishes naturally on mine tailings. We evaluated the bioaccumulation of Cu, Pb, and Zn in P. laevigata foliar tissue, the leaf micro- and macro-morphological characters, DNA damage, and population genetic effects. In total, 80 P. laevigata individuals (20/site) belonging to four populations: The individuals from both sites (exposed and reference) bioaccumulated HMs (Pb > Cu > Zn). However, in the exposed individuals, Pb and Cu bioaccumulation was significantly higher. Also, a significant effect of macro- and micro-morphological characters was registered, showing significantly lower values in individuals from the exposed sites. In addition, we found significant differences in genotoxic damage in P. laevigata individuals, between the exposed and reference sites. In contrast, for the micro-morphological characters, none of the analyzed metals had any influence. P. laevigata did not show significant differences in the genetic structure and diversity between exposed and reference populations. However, four haplotypes and four private alleles were found in the exposed populations. Since P. laevigata is a species that establishes naturally in polluted sites and bioaccumulates HM in its foliar tissues, the resulting genetic, individual and population effects have not been severe enough to show detrimental effects; hence, P. laevigata can be a useful tool in phytoremediation strategies for soils polluted with Pb and Cu, maintaining its important ecological functions.

The Effects of Climate Change on the Distribution Pattern of Species Richness of Endemic Wetland Plants in the Qinghai-Tibet Plateau.

Wetland ecosystems in the Qinghai-Tibet Plateau (QTP), the region with the richest biodiversity and the most important ecological barrier function at high altitudes, are highly sensitive to global change, and wetland plants, which are important indicators of wetland ecosystem structure and function, are also threatened by wetland degradation. Therefore, a comprehensive study of changes in the geographical distribution pattern of plant diversity, as well as species loss and turnover of wetlands in the QTP in the context of global climate change is of great importance for the conservation and restoration of wetland ecosystems in the QTP. In this study, species turnover and loss of 395 endemic wetland plants of the QTP were predicted based on the SSP2-4.5 climate change scenarios. The results showed that there were interspecific differences in the effects of climate change on the potential distribution of species, and that most endemic wetland plants would experience range contraction. Under the climate change scenarios, the loss of suitable wetland plant habitat is expected to occur mainly in parts of the southern, north-central and north-western parts of the plateau, while the gain is mainly concentrated in parts of the western Sichuan Plateau, the Qilian Mountains, the Three Rivers Source Region and the northern Tibetan Plateau. Overlaying the analysis of priority protected areas with the established protected areas in the QTP has resulted in the following conservation gaps: the eastern Himalayan region, midstream of the Yarlung Zangbo River, the transition zone between the northern Tibetan Plateau and the Hengduan Mountains, Minshan-Qionglai mountain, Anyemaqen Mountains (southeast) to Bayankala (southeast) mountains, the southern foothills of the Qilian Mountains and the northern Tibetan Plateau region. In the future, the study of wetland plant diversity in the QTP and the optimisation of protected areas should focus on the conservation gaps. This study is of great importance for the study and conservation of wetland plant diversity in the QTP, and also provides a scientific basis for predicting the response of wetland plants to climate change in the QTP.

Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2

BackgroundFungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be beneficial when administered as probiotics. In mycology, the internal transcribed spacer (ITS) region was adopted as the universal marker for classifying fungi. Hence, an accurate and robust method for ITS classification is not only desired for the purpose of better diversity estimation, but it can also help us gain a deeper insight into the dynamics of environmental communities and ultimately comprehend whether the abundance of certain species correlate with health and disease. Although many methods have been proposed for taxonomic classification, to the best of our knowledge, none of them fully explore the taxonomic tree hierarchy when building their models. This in turn, leads to lower generalization power and higher risk of committing classification errors.ResultsHere we introduce HiTaC, a robust hierarchical machine learning model for accurate ITS classification, which requires a small amount of data for training and can handle imbalanced datasets. HiTaC was thoroughly evaluated with the established TAXXI benchmark and could correctly classify fungal ITS sequences of varying lengths and a range of identity differences between the training and test data. HiTaC outperforms state-of-the-art methods when trained over noisy data, consistently achieving higher F1-score and sensitivity across different taxonomic ranks, improving sensitivity by 6.9 percentage points over top methods in the most noisy dataset available on TAXXI.ConclusionsHiTaC is publicly available at the Python package index, BIOCONDA and Docker Hub. It is released under the new BSD license, allowing free use in academia and industry. Source code and documentation, which includes installation and usage instructions, are available at https://gitlab.com/dacs-hpi/hitac.