Communities Of Soil Organisms Research Articles

Structure and function role of soil nematode communities in different types of vegetation in Yogyakarta and Central Java, Indonesia

Abstract. Indarti S, Utami SNH, Putra NS, Maharani R. 2024. Structure and function role of soil nematode communities in different types of vegetation in Yogyakarta and Central Java, Indonesia. Biodiversitas 25: 2765-2772. Soil nematodes are crucial parts of the soil organism community and play a significant role in many ecological soil processes. It is necessary to pay greater attention to the lack of knowledge regarding the composition and role of the soil nematode community in different vegetations. Hence, the nematode structure community from minimal to soil stillages have been observed and compared from seven distinct types of vegetation. This study aimed to determine the soil nematode community structure, which includes the dominance, abundance, richness, diversity, and functional role of nematodes, as well as other chemical soil properties. Vegetation type represents soil management and has an impact on the life of soil organisms such as nematodes. A total of approximately 2328 soil nematodes were found, and 18 genera were identified. The Nematode Indicator Joint Analysis (NINJA) revealed that the vegetation type, land use, and soil chemical properties influence the nematode’s abundance, dominance, and structure differently. Through those results, the authors confirmed that soil nematodes in cultivated vegetation are dominated by the trophic groups of plant-parasitic nematodes and bacterivores. Conversely, predator, omnivores, and fungivores nematodes dominate in soil with minimal tillage. Overall, this study highlights the importance of soil nematode analysis in sustainable agricultural soil ecosystems.

Divergent impacts of fertilization regimes on below-ground prokaryotic and eukaryotic communities in the Tibetan Plateau

Chemical nutrient amendment by human activities can lead to environmental impacts contributing to global biodiversity loss. However, the comprehensive understanding of how below- and above-ground biodiversity shifts under fertilization regimes in natural ecosystems remains elusive. Here, we conducted a seven-year field experiment (2011-2017) and examined the effects of different fertilization on plant biodiversity and soil belowground (prokaryotic and eukaryotic) communities in the alpine meadow of the Tibetan Plateau, based on data collected in 2017. Our results indicate that nitrogen addition promoted total plant biomass but reduced the plant species richness. Conversely, phosphorus enrichment did not promote plant biomass and exhibited an unimodal pattern with plant richness. In the belowground realm, distinct responses of soil prokaryotic and eukaryotic communities were observed under fertilizer application. Specifically, soil prokaryotic diversity decreased with nitrogen enrichment, correlating with shifts in soil pH. Similarly, soil eukaryotic diversity decreased with increased phosphorous inputs, aligning with the equilibrium between soil available and total phosphorus. We also established connections between these soil organism communities with above-ground plant richness and biomass. Overall, our study contributes to a better understanding of the sustainable impacts of human-induced nutrient enrichment on the natural environment. Future research should delve deeper into the long-term effects of fertilization on soil health and ecosystem functioning, aiming to achieve a balance between agricultural productivity and environmental conservation.

Strong above-ground impacts of a non-native ungulate do not cascade to impact below-ground functioning in a boreal ecosystem.

1. Experimental studies across biomes demonstrate that herbivores can have significant effects on ecosystem functioning. Herbivore effects, however, can be highly variable with studies demonstrating positive, neutral or negative relationships between herbivore presence and different components of ecosystems. Mixed effects are especially likely in the soil, where herbivore effects are largely indirect mediated through effects on plants. 2. We conducted a long-term experiment to disentangle the effects of non-native moose in boreal forests on plant communities, nutrient cycling, soil composition and soil organism communities. 3. To explore the effect of moose on soils, we conduct separate analyses on the soil organic and mineral horizons. Our data come from 11 paired exclosure-control plots in eastern and central Newfoundland, Canada that provide insight into 22-25 years of moose herbivory. We fit piecewise structural equations models (SEM) to data for the organic and mineral soil horizons to test different pathways linking moose to above-ground and below-ground functioning. 4. The SEMs revealed that moose exclusion had direct positive impacts on adult tree count and an indirect negative impact on shrub percent cover mediated by adult tree count. We detected no significant impact of moose on soil microbial C:N ratio or net nitrogen mineralization in the organic or mineral soil horizon. Soil temperature and moisture, however, was more than twice as variable in the presence (i.e. control) than absence (i.e. exclosure) of moose. Overall, we observed clear impacts of moose on above-ground forest components with limited indirect effects below-ground. Even after 22-25 years of exclusion, we did not find any evidence of moose impacts on soil microbial C:N ratio and net nitrogen mineralization. 5. Our long-term study and mechanistic path analysis demonstrates that soils can be resilient to ungulate herbivore effects despite evidence of strong effects above-ground. Long-term studies and analyses such as this one are relatively rare yet critical for reconciling some of the context-dependency observed across studies of ungulates effects on ecosystem functions. Such studies may be particularly valuable in ecosystems with short growing seasons such as the boreal forest.

Response of total belowground soil biota in Alhagi sparsifolia monoculture at different soil vertical profiles in desert ecosystem

The soil organisms are extremely important for the land-based ecosystem. There is a growing interest in studying the variety and composition of the entire underground soil organism community at a large ecological scale. Soil organisms show different patterns in relation to soil physiochemical properties (SPPs) in various ecosystems. However, there is limited knowledge regarding their response to soil vertical profiles (SVPs) in monoculture of Alhagi sparsifolia, which is the primary shrub in the deserts of China, and is well-known for its contributions to sand dune stabilization, traditional Chinese medicine, and forage. Here, we investigated the population dynamics of soil bacteria, fungi, archaea, protists and metazoa across six different SVPs ranging from 0 to 100 cm in monoculture of A. sparsifolia, in its natural desert ecosystem. Our findings indicate that the soil biota communities displayed a declining pattern in the alpha diversity of bacteria, protists, and metazoa with an increase in soil depth. However, the opposite trend was observed for fungi and archaea. The beta diversity of soil biota was significantly affected by SVPs, particularly for metazoa, fungi and protists as revealed by Non-Metric Dimensional Scaling. The most prevalent soil bacterial, fungal, archaeal, protist, and metazoa classes were Actinobacteria, Sordariomycetes, Nitrososphaeria, Filosa-Sarcomonadea, and Nematoda, respectively. The correlation among vertical distribution of the most abundant biotic communities and variations in SPPs exhibited that the variations in total carbon (TC) and total nitrogen (TN) had the most significant influence on bacterial changes, while available potassium (AK) had an impact on fungi. Archaea were affected by TC and pH, protists by the C/N-Ratio and TP, and metazoa by TN, AK, and soil water capacity (SWC). Collectively, our findings provide a new perspective on the vertical distribution and distinct response patterns of soil biota in A. sparsifolia monoculture under natural desert ecosystem of China.

Composition of Soil Bacterial and Nematode Communities within Soil Aggregates in a Kiwifruit Orchard under Cover Crop Treatment

Soil, which exhibits difference in nutrient contents and aggregate sizes, provides spatially distinct habitats for biota. Cover crops influence the compositions of soil organism communities, playing an indispensable role in regulation of underground food webs and ecosystem functions. However, the effect of cover crops on soil microbes and nematodes distribution within different aggregate sizes remains unknown. Thus, a field experiment in a kiwifruit orchard with cover crops was conducted to estimate the distribution of soil nematodes and bacteria with different soil aggregate sizes (mega-aggregate (>2 mm, LMA), macro-aggregate (0.25–2 mm, SMA), and micro-aggregate (<0.25 mm, MA)) and cover crop treatments (four cover crop species (CC) and no cover crop as control (CK)). The results showed that bacterial compositions varied with both aggregate sizes and cover crop treatments. The composition of bacterial community was significantly different between mega-aggregate and micro-aggregate, and bacterial community diversity was significantly higher in micro-aggregate compared with mega-aggregate. Moreover, cover crop treatment dramatically changed the compositions of bacterial communities. However, the nematode communities were mainly impacted by soil aggregate sizes. Larger aggregates (mega- and macro-aggregates) contained higher abundance of omnivores/predators and lower abundance of fungivores. In contrast to bacterial community, the richness of nematode community was lower in micro-aggregates compared with larger aggregates (mega- and macro-aggregates). Redundancy analysis (RDA) and structural equation model (SEM) showed soil organic carbon (SOC) was the main soil factor that directly and indirectly affected both bacterial and nematode communities. The investigations of both bacterial and nematode communities could provide a better understanding on carbon and nutrient cycling across aggregate size fractions.

Soil microarthropod distribution on the urban–rural gradient of Riga city: a study with robust sampling method application

AbstractTo address the new challenge of bringing more nature into the urban environment and developing adequate green infrastructure management methods, it is necessary to clarify the regularities of the distribution of the main ecosystem components—soil organism communities on the urban gradient. Microarthropods—collembolans and mites—are the most diverse soil animals and bioindicators of soil conditions. However, no suitable approaches exist so far to help reduce the high workload of soil zoological studies and make the data acquisition for soil assessment faster. To get closer to a solution to this problem, we propose a robust sampling approach using one pooled sample per site with surface area 58 cm2. This was tested in a microarthropod distribution study on the urban gradient of Riga city (Latvia) in six urban habitat types at 21 sites. The use of classical statistical methods for the processing of soil microarthropod data is limited because these data do not meet model requirements on which classical methods are based, first of all, conformity to the normal distribution. These problems are circumvented by bootstrapping methodology, which thanks to increasing computer performance now is implemented in the most modern program packages. We tested a set of such methods: one-way bootstrap-based analysis of variance, nonmetric multidimensional scaling (NMS), nonparametric multiplicative regression (NPMR), multi-response permutation procedure and Chao bootstrap-based rarefaction curves. NMS in combination with NPMR gave the best results providing statistically significant species distribution curves along the urban gradient which were broadly in line with species traits found by other studies.

Sympatric soil biota mitigate a warmer-drier climate for Bouteloua gracilis.

Climate change is altering temperature and precipitation, resulting in widespread plant mortality and shifts in plant distributions. Plants growing in soil types with low water holding capacity may experience intensified effects of reduced water availability as a result of climate change. Furthermore, complex biotic interactions between plants and soil organisms may mitigate or exacerbate the effects of climate change. This 3-year field experiment observed the performance of Bouteloua gracilis ecotypes that were transplanted across an environmental gradient with either sympatric soil from the seed source location or allopatric soil from the location that plants were transplanted into. We also inoculated plants with either sympatric or allopatric soil biotic communities to test: (1) how changes in climate alone influence plant growth, (2) how soil types interact with climate to influence plant growth, and (3) the role of soil biota in mitigating plant migration to novel environments. As expected, plants moved to cooler-wetter sites exhibited enhanced growth; however, plants moved to warmer-drier sites responded variably depending on the provenance of their soil and inoculum. Soil and inoculum provenance had little influence on the performance of plants moved to cooler-wetter sites, but at warmer-drier sites they were important predictors of plant biomass, seed set, and specific leaf area. Specifically, transplants inoculated with their sympatric soil biota and grown in their sympatric soil were as large as or larger than reference plants grown at the seed source locations; however, individuals inoculated with allopatric soil biota were smaller than reference site individuals at warmer, drier sites. These findings demonstrate complicated plant responses to various aspects of environmental novelty where communities of soil organisms may help ameliorate stress. The belowground microbiome of plants should be considered to predict the responses of vegetation more accurately to climate change.

Traditional and cover crop-derived mulches enhance soil ecosystem services in apple orchards

Organic mulches are a traditional method of groundcover management in temperate commercial orchards, now largely replaced by herbicides and synthetic fertilisers. As a potential contribution to improving orchard sustainability, we hypothesised that the addition of organic mulches would: (H1) improve soil fertility and lead to greater tree growth and yields; (H2) support a larger and more biologically active community of soil organisms, assessed as increased soil respiration and greater earthworm numbers and biomass; and (H3) increase leaf litter decomposition and burial, potentially reducing the risk of apple scab disease ( Venturia inaequalis ). Cuttings from two legume-based cover crop mixtures grown in the alleyway spaces between tree rows and two traditional mulch materials, straw and compost, were trialled alongside a bare soil business-as-usual control for two years, using a randomized complete block design in a conventionally managed commercial ‘Gala’ apple orchard in the UK. Compared to the control, the compost mulch significantly increased both soil carbon and nitrogen by over 50 %. The straw mulch effectively suppressed weeds by about 90 % and increased soil moisture by about 5 %. Cover crop cuttings increased moisture levels and increased earthworm numbers and mass by 1.7 and 1.8 times greater respectively in the double-rate ‘legume-grass’ cuttings treatment. Increasing the quantity of cover crop cuttings produced more positive effects; the cumulative addition of cuttings can benefit several soil-derived ecosystem services. This study took place in a commercial apple orchard, the findings may therefore be applicable to other orchard and row-grown perennial crops. • Mulches can improve soil moisture, soil carbon and nitrogen, and weed suppression. • Cuttings from orchard alleyway cover crops can be used as cost-effective mulches. • Cover crop-derived mulches can increase earthworm abundance and mass. • Organic mulches can support greater soil biota and soil biological activity. • Mulches can increase the decomposition of disease-harbouring leaf litter.

The ecological clusters of soil organisms drive the ecosystem multifunctionality under long-term fertilization.

Long-term fertilization is known to impact the biodiversity and community structures of soil organisms, which are responsible for multiple soil ecosystem functions (multifunctionality). However the relationship between the alterations of soil organisms and ecosystem multifunctionality remains unclear, especially in the case of long-term fertilization. To explore the contribution of soil organismal biodiversity and community structures to ecosystem multifunctionality, we took soil samples from a nearly 25-year field fertilization experiment. Organic matter significantly improved the soil ecosystem multifunctionality. Ecosystem multifunctionality was found to be closely linked to the biodiversity and communities of soil organisms within the major ecological clustering of soil organisms (Module 1) according to the trophic co-occurrence network, rather than the entire community of soil organisms. This indicated that ecological clusters of soil organisms within the network were critical in maintaining soil ecosystem multifunctionality. The application of organic fertilization could enrich specialized soil organisms and increase interactions of soil organisms in the ecological cluster. As a result, our findings emphasize the role of ecological clusters in the soil organismal co-occurrence network in controlling soil multifunctionality after long-term fertilization, presenting a novel perspective on the link between soil biodiversity and ecosystem multifunctionality.

A comparison of soil nematode community structure and environmental factors along fen-bush-forest succession in a peatland, northeastern China

Soil nematodes are one of the key components of the soil organism community and one of the major players in soil functions. The lack of knowledge in the structure and function of the soil nematode community in peatland succession needs to be given more attention. The soil nematode community structure including abundance, richness, diversity, and many ecological indices as well as soil factors were measured and compared in three different habitats along a natural fen-bush-forest successional sere in a peatland, northeastern China. A total of 36 soil nematode genera were identified, and multivariate analysis separated the three habitat samples from each other. The abundance, richness, and diversity increased from fen to forest. The dominant trophic group changed from bacterivores in the fen and bush to bacterivores and plant parasites in the forest. According to the RDA analysis with soil properties, it was found that the community structure of soil nematodes in the fen was more affected by the soil nitrogen content, by soil C/N ratio in the bush, and by soil phosphorus content and soil pH in the forest, respectively. Though the nematode channel ratio in three habitats indicated that the energy flow in the soil micro-food web was all dominated by bacterial channels, the trophic group with the highest metabolic footprints was bacterivores in the bush but omnivore-predators (Op) in fen and forest. This study demonstrated that the community composition and trophic structure of soil nematodes as well as the predominant environmental factors significantly changed along fen-bush-forest successional sere. The genera Udonchus and Eudorylaimus may have the potentials to be indicators of vegetation succession and soil microbe food web in fens.

Trees and herbaceous vegetation strips both contribute to changes in soil fertility and soil organism communities in an agroforestry system

Alley cropping systems introduce herbaceous strips planted with trees into cropped fields. While such systems may have a positive effect on soil fertility, the respective roles of the trees and the herbaceous vegetation in shaping this effect remain unclear. We investigated the effect of the distance from herbaceous strips with or without walnut trees on soil fertility and earthworm communities in a 20 year old Mediterranean plot intercropped with tomatoes. We determined the effects of i) the presence of trees, ii) the distance from the herbaceous strip (0 m, 1 m and 2.5 m) and iii) the distance from the tree on microbial biomass and respiration, earthworm density and soil C, N and P contents in the 0–25 cm layer at three sampling seasons. Herbaceous strips presented a higher microbial biomass C related to soil organic carbon, a lower microbial metabolic quotient, and a higher density of earthworms than the crop alley regardless of tree presence. Soil organic carbon content increased in the presence of trees. Available P and microbial biomass increased at 1 m from the tree in the HS. Earthworm density and microbial biomass were higher at 1 m than at 2.5 m from the HS. Herbaceous strips were an effective shelter for earthworms and fostered a high and efficient microbial biomass throughout the year, with or without trees, probably due to diversified vegetation and no soil disturbance. The mechanisms by which these changes could impact the crop alley remain to be studied.

DNA metabarcoding illuminates the black box of soil animal biodiversity

Identifying the determinants of the distribution of soil organism communities at different spatial scales is essential to our understanding of the functioning of terrestrial ecosystems. Indeed, spatial patterns of soil biota, and the factors that determine them, influence spatial patterns of many ecological processes such as the decomposition of organic detritus, the release of nutrients and, ultimately, the spatial structure of plant communities (Ettema & Wardle, 2002). However, our ability to describe and understand the spatial distribution of soil communities is severely hampered by taxonomic and methodological limitations, significantly reducing our ability to infer ecological and evolutionary mechanisms from observed patterns. In a From the Cover article in this issue of Molecular Ecology, Arribas et al. (2020) used a high‐throughput sequencing approach, i.e., haplotype‐level‐COI metabarcoding, to bypass these road blocks and analyse the spatial arrangements of soil arthropods communities at different phylogenetic levels, from haplotypes to nested operational units. They found that local assemblage composition was primarily explained by habitat, and that community similarity decreased with distance in a similar way in all habitats and geographical regions, and at all hierarchical levels. This highlights that both habitat filtering and dispersal limitation are major drivers of local‐scale assembly process in soil arthropod communities. Beyond these significant results, their study also highlights how DNA‐based approaches, by producing combined description of genetic and taxonomic diversity, opens up new perspectives to soil spatial ecology and macroecology.

Dynamics of community structure and bio-thermodynamic health of soil organisms following subtropical forest succession

Soil organisms play essential roles in maintaining multiple ecosystem processes, but our understanding of the dynamics of these communities during forest succession remains limited. In this study, the dynamics of soil organism communities were measured along a 3-step succession sequence of subtropical forests (i.e., a conifer forest, CF; a mixed conifer and broad-leaved forest, MF; and a monsoon evergreen broad-leaved forest, BF). The eco-exergy evaluation method was used as a complement to the classic community structure index system to reveal the holistic dynamics of the bio-thermodynamic health of soil organism communities in a forest succession series. Association between the self-organization of soil organisms, soil properties, and plant factors were explored through redundancy analyses (RDA). The results indicated that the biomass of soil microbes progressively increased in the dry season, from 0.75gm-2 in CF to 1.75gm-2 in BF. Microbial eco-exergy showed a similar pattern, while the community structure and the specific eco-exergy remained constant. Different trends for the seasons were observed for the soil fauna community, where the community biomass increased from 0.72gm-2 to over 1.97gm-2 in the dry season, but decreased from 3.94gm-2 to 2.36gm-2 in the wet season. Faunal eco-exergies followed a similar pattern. Consequently, the average annual biomass of the soil faunal community remained constant (2.17-2.39gm-2) along the forest succession sequence, while the significant seasonal differences in both faunal biomass and eco-exergy observed at the early successional stage (CF) were insignificant in the middle and late forest successional stages (MF and BF). Both the dynamics of soil microbes and soil fauna were tightly correlated with tree biomass and with soil physicochemical properties, especially soil pH, moisture, total nitrogen, nitrate nitrogen, and organic matter content.

Field management of Rotylenchulus reniformis on pineapple combining crop rotation, chemical-mediated induced resistance and endophytic bacterial inoculation

In Martinique or La Réunion, French authorities recently banned the use of pesticides for the management of “soil-borne pathogens” on pineapple after several decades of intensive monoculture where the natural balance between beneficial and harmful communities of soil organisms has disappeared. Today, increasing infestation of pineapple by the nematode R. reniformis and other “soil-borne pathogens” causes severe damage to the crop. New cropping systems with innovative ecological nematode management are needed. An eco-friendly cropping system, which comprised rotation of sunn hemp ( C. juncea ), pineapple, a natural grass fallow and another cash crop, eggplant, consistently reduced the inoculum of nematodes. Nematode populations were reduced by 86.4%, 82% and 46.5% respectively under pineapple, sunn hemp and grass fallow compared to infestations of eggplant (3456 nematodes .100g -1 of soil) after several rotations. Integrating a chemical induction of systemic resistance or application of an endophytic bacteria recovered from pineapple roots, Bacillus sp . GVS2, helped maintain low populations of nematodes during the vegetative cycle. On two pineapple varieties, MD2 and Victoria (Queen), two different treatments were applied monthly in the field, methyl jasmonate (10 −4 M, 10 ml per plant), or a suspension of Bacillus sp. GVS2 (10 8 CFU ml −1 , 10 ml per plant) isolated from pineapple roots. After eight months, the nematode populations were reduced respectively on MD2 and Victoria (Queen) by 58.3% and 50.3% with the methyl jasmonate and by 59.6% and 54.3% with the Bacillus sp. GVS2 compared to controls. Because of the efficiency of sunn hemp in reducing the inoculum of nematodes, no significant differences in vegetative growth were observed using the D leaf weight and the estimated root length densities (RLD). The potential of pest management through eco-friendly cropping systems for pineapple with a biocontrol for nematodes with no pesticide is discussed. • Eco-friendly pineapple cropping systems are potential alternative to pesticides. • Pineapple - Crotalaria rotations reduces R. reniformis infestation. • Induced systemic resistances were shown to be efficient on pineapple nematodes in field. • An endophytic bacteria Bacillus sp. GVS2 reduced R. reniformis multiplication.

Do soil inoculants accelerate dryland restoration? A simultaneous assessment of biocrusts and mycorrhizal fungi

Biological soil crusts (biocrusts) and arbuscular mycorrhizal (AM) fungi are communities of soil organisms often targeted to assist in the achievement of multiple ecological restoration goals. In drylands, benefits conferred from biocrust and AM fungal inoculation, such as improved native plant establishment and soil stabilization, have primarily been studied separately. However, comparisons between these two types of soil inoculants and investigations into potential synergies between them, particularly at the plant community scale, are needed to inform on‐the‐ground management practices in drylands. We conducted two full‐factorial experiments—one in greenhouse mesocosms and one in field plots—to test the effects of AM fungal inoculation, biocrust inoculation, and their interaction on multiple measures of dryland restoration success. Biocrust inoculation promoted soil stabilization and plant drought tolerance, but had mixed effects on native plant diversity (positive in greenhouse, neutral in field) and productivity (negative in greenhouse, neutral in field). In greenhouse mesocosms, biocrust inoculation reduced plant biomass, which was antagonistic to % root length colonized by AM fungi. Inoculation with native or commercial AM fungi did not influence plant establishment, drought tolerance, or soil stabilization in either study, and few synergistic effects of simultaneous inoculation of AM fungi and biocrusts were observed. These results suggest that, depending on the condition of existing soil communities, inoculation with AM fungi may not be necessary to promote dryland restoration goals, while inoculation with salvaged biocrust inoculation may be beneficial in some contexts.

Effect of coupled reduced irrigation and nitrogen fertilizer on soil mite community composition in a wheat field.

Groundwater and nitrogen fertilizer overuse severely threatens crop productions; thus, current ecological agriculture requires low irrigation and nitrogen fertilizer inputs. The effects of combined reduced irrigation and nitrogen fertilizer addition on soil organism (e.g., mite) community and biodiversity remain poorly understood. We analyzed soil mite community composition, wheat grain yield, and soil characteristics in a 10‐year manipulation experiment with two levels of irrigation (reduced and conventional irrigation) and five nitrogen fertilizer levels (0, 70, 140, 210, and 280 kg N/ha). Reduced irrigation (20% reduction, from 280 to 220 mm) and nitrogen fertilizer (25% reduction, from 280 to 210 kg N/ha) addition did not significantly influence soil mite community and wheat yield. The relative abundances of fungivores and predators showed negative quadratic relationships with wheat yield, while that of plant parasites showed a positive relationship. The relationships between soil mite trophic groups and wheat yield revealed that we can evaluate the impacts of reduced irrigation and nitrogen fertilizer addition from the perspective of soil fauna. Soil mite community composition was altered by soil abiotic factors prior to reduced irrigation and nitrogen fertilizer addition. Overall, moderate reductions of irrigation and nitrogen fertilizer may not threaten to soil mite community and diversity or decrease crop production; in contrast, such reductions will benefit mite community development and the sustainable agriculture.

Soil microbial community assemblage and its seasonal variability in alpine treeline ecotone on the eastern Qinghai-Tibet Plateau

The alpine treeline ecotone is characterized as the upper limit of the forest in the high-mountain ecosystem. Due to the freeze-thaw cycles, the soil organism community, such as microbial communities are expected to change between seasons. However, there are limited microbial-community studies focused on the high altitude alpine ecosystem. We conducted a study in the alpine treeline ecotone on the eastern Qinghai-Tibet Plateau, China, and investigated the seasonal variability of the soil microbial community. We collected all soil samples within the alpine treeline ecotone, between the treeline and timberline in the high-mountain region. The 16S rRNA genes of the microbial communities (bacterial and archaeal) were analyzed by high-throughput sequencing to the genus level. The results showed that soil microbial community in the alpine treeline ecotone was consistently dominated by eight phyla which consisted of 95% of the total microbial community, including Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Chloroflexi, Bacteroidetes, and Verrucomicrobia. The overall diversity and evenness of the community were relatively stable, with an average of 0.5% difference between seasons. The highest seasonal variability occurred at the upper boundary of the alpine treeline ecotone, and few or almost no seasonal change was observed at lower elevations, indicating dense forest cover and litter deposition might have created a local microclimate that reduced seasonal variation among the surrounding environmental conditions. Our study was one of the first group that documented the microbial community assemblage in the treeline ecotone on the Qinghai-Tibet Plateau.

Do soil biota influence the outcome of novel interactions between plant competitors?

1. Species are shifting their ranges, for example to higher elevations, in response to climate change. Different plant species and soil microbiota will likely shift their ranges at different rates, giving rise to novel communities of plants and soil organisms. However, the ecological consequences of such novel plant-soil interactions are poorly understood. We experimentally simulated scenarios for novel interactions arising between high- and low elevation plants and soil biota following asynchronous climate change range shifts, asking to what extent the ability of plants to coexist depends on the origin of the soil biota. 2. In a greenhouse experiment, we grew pairs of low- (Poa trivialis and Plantago lanceolata) and high- (Poa alpina and Plantago alpina) elevation plant species alone and against a density gradient of con- or heterospecific neighbours. Plants grew on sterilized field soil that was inoculated with a soil community sampled from either low- or high elevation in the western Swiss Alps. We used the experiment to parameterize competition models, from which we predicted the population-level outcomes of competition in the presence of the different soil biota. 3. In the absence of neighbours, three of the four species produced more biomass with the low elevation soil biota. As a result of generally similar responses across plant species, soil biota tended not to affect plant interaction outcomes, with the low elevation species generally predicted to competitively exclude high elevation species irrespective of the soil biota origin. However, the low elevation grass Poa trivialis was only able to invade communities of Poa alpina in the presence of a low elevation soil biota. This suggests that, at least in some cases, the outcome of novel competitive interactions between plants following climate change will depend on whether shifts in the distribution of plant and soil organisms are asynchronous. 4. Synthesis. Our results indicate that the changing soil communities that plants encounter during range expansion can influence plant performance. However, this is only likely to alter expectations for the ability of plants to coexist following climate change if plant species respond differently to the change in the soil community.

Soil chemistry changes beneath decomposing cadavers over a one-year period

Decomposing vertebrate cadavers release large, localized inputs of nutrients. These temporally limited resource patches affect nutrient cycling and soil organisms. The impact of decomposing cadavers on soil chemistry is relevant to soil biology, as a natural disturbance, and forensic science, to estimate the postmortem interval. However, cadaver impacts on soils are rarely studied, making it difficult to identify common patterns. We investigated the effects of decomposing pig cadavers (Sus scrofa domesticus) on soil chemistry (pH, ammonium, nitrate, nitrogen, phosphorous, potassium and carbon) over a one-year period in a spruce-dominant forest. Four treatments were applied, each with five replicates: two treatments including pig cadavers (placed on the ground and hung one metre above ground) and two controls (bare soil and bags filled with soil placed on the ground i.e. "fake pig" treatment). In the first two months (15-59 days after the start of the experiment), cadavers caused significant increases of ammonium, nitrogen, phosphorous and potassium (p<0.05) whereas nitrate significantly increased towards the end of the study (263-367 days; p<0.05). Soil pH increased significantly at first and then decreased significantly at the end of the experiment. After one year, some markers returned to basal levels (i.e. not significantly different from control plots), whereas others were still significantly different. Based on these response patterns and in comparison with previous studies, we define three categories of chemical markers that may have the potential to date the time since death: early peak markers (EPM), late peak markers (LPM) and late decrease markers (LDM). The marker categories will enhance our understanding of soil processes and can be highly useful when changes in soil chemistry are related to changes in the composition of soil organism communities. For actual casework further studies and more data are necessary to refine the marker categories along a more precise timeline and to develop a method that can be used in court.

Standard methods for the assessment of structural and functional diversity of soil organisms: A review.

The lack of standardized methods to study soil organisms prevents comparisons across data sets and the development of new global and regional experiments and assessments. Moreover, standardized methods are needed to evaluate the impact of anthropogenic stressors, such as chemicals, on soil organism communities in the regulatory context. The goal of this contribution is to summarize current methodological approaches to measure structural and functional diversity of soil organisms, and to identify gaps and methodological improvements so as to cross data sets generated worldwide. This is urgently needed because several currently ongoing regional and global soil biodiversity studies are not coordinated with one another in terms of methodology, including database development. Therefore, we evaluated the standard methods to sample, identify, determine, and assess soil organisms currently applied or proposed, using well-accepted criteria such as ecological relevance; practicability of usage in terms of resources, time, and costs; and the level of standardization. Methods addressing both the structure and the functions of soil organisms (populations or communities) are included, with a special focus on new molecular methods based on nucleic acid extraction and further analyses by polymerase chain reaction (PCR)-based approaches for microorganisms and invertebrates. We particularly highlight the activities of the Technical Committee (TC) 190 of the International Organization for Standardization (ISO) because ISO guidelines are legally accredited by many national or international authorities when they put conservation laws and regulations into practice. Finally, we propose detailed recommendations regarding gaps in the available set of standards, in order to identify a list of new methods to be standardized. We propose to organize this whole process under the Global Soil Biodiversity Initiative (GSBI) in order to ensure a truly global approach for the assessment of soil biodiversity. Integr Environ Assess Manag 2018;14:463-479. © 2018 SETAC.