Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics

Understanding the relationship between soil microbial taxonomic compositions and functional profiles is essential for predicting ecosystem functions under various environmental disturbances. However, even though microbial communities are sensitive to disturbance, ecosystem functions remain relatively stable, as soil microbes are likely to be functionally redundant. Microbial functional redundancy may be more associated with “broad” functions carried out by a wide range of microbes, than with “narrow” functions specialized by specific microorganisms. Thus, a comprehensive study to evaluate how microbial taxonomic compositions correlate with “broad” and “narrow” functional profiles is necessary. Here, we evaluated soil metagenomes worldwide to assess whether functional and taxonomic diversities differ significantly between the five “broad” and the five “narrow” functions that we chose. Our results revealed that compared with the five “broad” functions, soil microbes capable of performing the five “narrow” functions were more taxonomically diverse, and thus their functional diversity was more dependent on taxonomic diversity, implying lower levels of functional redundancy in “narrow” functions. Co-occurrence networks indicated that microorganisms conducting “broad” functions were positively related, but microbes specializing “narrow” functions were interacting mostly negatively. Our study provides strong evidence to support our hypothesis that functional redundancy is significantly different between “broad” and “narrow” functions in soil microbes, as the association of functional diversity with taxonomy were greater in the five “narrow” rather than the five “broad” functions.

Potentially Toxic Elements’ Contamination of Soils Affected by Mining Activities in the Portuguese Sector of the Iberian Pyrite Belt and Optional Remediation Actions: A Review

Both sectors of the Iberian Pyrite Belt, Portuguese and Spanish, have been exploited since ancient times, but more intensively during and after the second half of the 19th century. Large volumes of polymetallic sulfide ore were extracted in open pits or in underground works, processed without environmental concerns, and the generated waste rocks and tailings were simply deposited in the area. Many of these mining sites were abandoned for years under the action of erosive agents, leading to the spread of trace elements and the contamination of soils, waters and sediments. Some of these mine sites have been submitted to rehabilitation actions, mostly using constructive techniques to dig and contain the contaminated tailings and other waste materials, but the remaining soil still needs to be treated with the best available techniques to recover its ecosystem functions. Besides the degraded physical structure and poor nutritional status of these soils, they have common characteristics, as a consequence of the pyrite oxidation and acid drainage produced, such as a high concentration of trace elements and low pH, which must be considered in the remediation plans. This manuscript aims to review the results from studies which have already covered these topics in the Iberian Pyrite Belt, especially in its Portuguese sector, considering: (i) soils’ physicochemical characteristics; (ii) potentially toxic trace elements’ concentration; and (iii) sustainable remediation technologies to cope with this type of soil contamination. Phytostabilization, after the amelioration of the soil’s properties with organic and inorganic amendments, was investigated at the lab and field scale by several authors, and their results were also considered.

Global monitoring of soil animal communities using a common methodology

Here we introduce the Soil BON Foodweb Team, a cross-continental collaborative network that aims to monitor soil animal communities and food webs using consistent methodology at a global scale. Soil animals support vital soil processes via soil structure modification, direct consumption of dead organic matter, and interactions with microbial and plant communities. Soil animal effects on ecosystem functions have been demonstrated by correlative analyses as well as in laboratory and field experiments, but these studies typically focus on selected animal groups or species at one or few sites with limited variation in environmental conditions. The lack of comprehensive harmonised large-scale soil animal community data including microfauna, mesofauna, and macrofauna, in conjunction with related soil functions, limits our understanding of biological interactions in soil communities and how these interactions affect ecosystem functioning. To provide such data, the Soil BON Foodweb Team invites researchers worldwide to use a common methodology to address six long-term goals: (1) to collect globally representative harmonised data on soil micro-, meso-, and macrofauna communities; (2) to describe key environmental drivers of soil animal communities and food webs; (3) to assess the efficiency of conservation approaches for the protection of soil animal communities; (4) to describe soil food webs and their association with soil functioning globally; (5) to establish a global research network for soil biodiversity monitoring and collaborative projects in related topics; (6) to reinforce local collaboration networks and expertise and support capacity building for soil animal research around the world. In this paper, we describe the vision of the global research network and the common sampling protocol to assess soil animal communities and advocate for the use of standard methodologies across observational and experimental soil animal studies. We will use this protocol to conduct soil animal assessments and reconstruct soil food webs on the sites included in the global soil biodiversity monitoring network, Soil BON, allowing us to assess linkages among soil biodiversity, vegetation, soil physico-chemical properties, and ecosystem functions. In the present paper, we call for researchers especially from countries and ecoregions that remain underrepresented in the majority of soil biodiversity assessments to join us. Together we will be able to provide science-based evidence to support soil biodiversity conservation and functioning of terrestrial ecosystems.

Species losses, gains, and changes in persistent species are associated with distinct effects on ecosystem functioning in global grasslands

Global change drivers such as anthropogenic nutrient inputs simultaneously alter biodiversity, species composition, and ecosystem functions such as above ground biomass. These changes are interconnected by complex feedbacks among extinction, invasion, and shifting relative abundance. Here, we use a novel temporal application of the Price equation to separate species richness and biomass change through time and quantify the functional contributions of species that are lost, gained, and persist under ambient and experimental nutrient addition in 59 global grasslands. Under ambient conditions, compositional and biomass turnover was high, but species losses (i.e., local extinctions) were balanced by gains (i.e. colonization). Under fertilization, there was biomass loss associated with species loss. Few species were gained in fertilized conditions over time but those that were, and species that persisted, contributed to net biomass gains, outweighing biomass loss. These components of community change are associated with distinct effects on measures of ecosystem functioning.

Trophic and symbiotic links between obligate-glacier water bears (Tardigrada) and cryoconite microorganisms

Insights into biodiversity and trophic webs are important for understanding ecosystem functions. Although the surfaces of glaciers are one of the most productive and biologically diverse parts of the cryosphere, the links between top consumers, their diet and microbial communities are poorly understood. In this study, for the first time we investigated the relationships between bacteria, fungi and other microeukaryotes as they relate to tardigrades, microscopic metazoans that are top consumers in cryoconite, a biologically rich and productive biogenic sediment found on glacier surfaces. Using metabarcoding (16S rDNA for bacteria, ITS1 for fungi, and 18S rDNA for other microeukaryotes), we analyzed the microbial community structures of cryoconite and compared them with the community found in both fully fed and starved tardigrades. The community structure of each microbial group (bacteria, fungi, microeukaryotes) were similar within each host group (cryoconite, fully fed tardigrades and starved tardigrades), and differed significantly between groups, as indicated by redundancy analyses. The relative number of operational taxonomic units (ZOTUs, OTUs) and the Shannon index differed significantly between cryoconite and tardigrades. Species indicator analysis highlighted a group of microbial taxa typical of both fully fed and starved tardigrades (potential commensals), like the bacteria of the genera Staphylococcus and Stenotrophomonas, as well as a group of taxa typical of both cryoconite and fully fed tardigrades (likely part of the tardigrade diet; bacteria Flavobacterium sp., fungi Preussia sp., algae Trebouxiophyceae sp.). Tardigrades are consumers of bacteria, fungi and other microeukaryotes in cryoconite and, being hosts for diverse microbes, their presence can enrich the microbiome of glaciers.

Natural Afforestation on Abandoned Agricultural Lands during Post-Soviet Period: A Comparative Landsat Data Analysis of Bordering Regions in Russia and Belarus

Remote monitoring of natural afforestation processes on abandoned agricultural lands is crucial for assessments and predictions of forest cover dynamics, biodiversity, ecosystem functions and services. In this work, we built on the general approach of combining satellite and field data for forest mapping and developed a simple and robust method for afforestation dynamics assessment. This method is based on Landsat imagery and index-based thresholding and specifically targets suitability for limited field data. We demonstrated method’s details and performance by conducting a case study for two bordering districts of Rudnya (Smolensk region, Russia) and Liozno (Vitebsk region, Belarus). This study area was selected because of the striking differences in the development of the agrarian sectors of these countries during the post-Soviet period (1991-present day). We used Landsat data to generate a consistent time series of five-year cloud-free multispectral composite images for the 1985–2020 period via the Google Earth Engine. Three spectral indices, each specifically designed for either forest, water or bare soil identification, were used for forest cover and arable land mapping. Threshold values for indices classification were both determined and verified based on field data and additional samples obtained by visual interpretation of very high-resolution satellite imagery. The developed approach was applied over the full Landsat time series to quantify 35-year afforestation dynamics over the study area. About 32% of initial arable lands and grasslands in the Russian district were afforested by the end of considered period, while the agricultural lands in Belarus’ district decreased only by around 5%. Obtained results are in the good agreement with the previous studies dedicated to the agricultural lands abandonment in the Eastern Europe region. The proposed method could be further developed into a general universally applicable technique for forest cover mapping in different growing conditions at local and regional spatial levels.

Plant-Soil Feedbacks for the Restoration of Degraded Mine Lands: A Review

Much effort has been made to remediate the degraded mine lands that bring severe impacts to the natural environments. However, it remains unclear what drives the recovery of biodiversity and ecosystem functions, making the restoration of these fragile ecosystems a big challenge. The interactions among plant species, soil communities, and abiotic conditions, i.e., plant-soil feedbacks (PSFs), significantly influence vegetation development, plant community structure, and ultimately regulate the recovery of ecosystem multi-functionality. Here, we present a conceptual framework concerning PSFs patterns and potential mechanisms in degraded mine lands. Different from healthy ecosystems, mine lands are generally featured with harsh physical and chemical properties, which may have different PSFs and should be considered during the restoration. Usually, pioneer plants colonized in the mine lands can adapt to the stressful environment by forming tolerant functional traits and gathering specific soil microbial communities. Understanding the mechanisms of PSFs would enhance our ability to predict and alter both the composition of above- and below-ground communities, and improve the recovery of ecosystem functions in degraded mine lands. Finally, we put forward some challenges of the current PSFs study and discuss avenues for further research in the ecological restoration of degraded mine lands.

Linking the effects of plant protection products on biodiversity and ecological processes to potential impairment of ecosystem functions and services—A multidisciplinary conceptual framework.

There is growing interest in using the ecosystem services framework for environmental risk assessments of plant protection products (PPP). However, there is still a broad gap between most of the ecotoxicological endpoints used in PPP risk assessment and the evaluation of the risks and effects of PPP on ecosystem services. Here we propose a conceptual framework to link current and future knowledge on the ecotoxicological effects of PPP on biodiversity and ecological processes to their consequences on ecosystem functions and services. We first describe the main processes governing the relationships between biodiversity, ecological processes and ecosystem functions in response to effects of PPP. We define 12 main categories of ecosystem functions that could be directly linked with the ecological processes used as functional endpoints in investigations on the ecotoxicology of PPP. An exploration of perceptions on the possible links between these categories of ecosystem functions and groups of ecosystem services (by a panel scientific experts in various fields of environmental sciences) then finds that these direct and indirect linkages still need clarification. We illustrate how the proposed framework could be used on terrestrial microalgae and cyanobacteria to assess the potential effects of herbicides on ecosystem services. The framework proposed here uses a set of clearly-defined core categories of ecosystem functions and services, which should help identify which of them are effectively or potentially threatened by PPP. We argue that this framework could help harmonize and extend the scientific knowledge that informs decision-making and policy-making.