Enumerating soil biodiversity.

Soil is an immense habitat for diverse organisms across the tree of life, but just how many organisms live in soil is surprisingly unknown. Previous efforts to enumerate soil biodiversity consider only certain types of organisms (e.g., animals) or report values for diverse groups without partitioning species that live in soil versus other habitats. Here, we reviewed the biodiversity literature to show that soil is likely home to 59 ± 15% of the species on Earth. We therefore estimate an approximately two times greater soil biodiversity than previous estimates, and we include representatives from the simplest (microbial) to most complex (mammals) organisms. Enchytraeidae have the greatest percentage of species in soil (98.6%), followed by fungi (90%), Plantae (85.5%), and Isoptera (84.2%). Our results demonstrate that soil is the most biodiverse singular habitat. By using this estimate of soil biodiversity, we can more accurately and quantitatively advocate for soil organismal conservation and restoration as a central goal of the Anthropocene.

Dissipation of pesticides and responses of bacterial, fungal and protistan communities in a multi-contaminated vineyard soil.

The effect of pesticide residues on non-target microorganisms in multi-contaminated soils remains poorly understood. In this study, we examined the dissipation of commonly used pesticides in a multi-contaminated vineyard soil and its effect on bacterial, fungal, and protistan communities. We conducted laboratory soil microcosm experiments under varying temperature (20°C and 30°C) and water content (20 % and 40 %) conditions. Pesticide dissipation half-lives ranged from 27 to over 300 days, depending on the physicochemical properties of the pesticides and the soil conditions. In both autoclaved and non-autoclaved soil experiments, over 50 % of hydrophobic pesticides (dimethomorph > isoxaben > simazine = atrazine = carbendazim) dissipated within 200 days at 20°C and 30°C. However, the contribution of biodegradation to the overall dissipation of soluble pesticides (rac-metalaxyl > isoproturon = pyrimethanil > S-metolachlor) increased to over 75 % at 30°C and 40 % water content. This suggests that soluble pesticides became more bioavailable, with degradation activity increasing with higher temperature and soil water content. In contrast, the primary process contributing to the dissipation of hydrophobic pesticides was sequestration to soil. High-throughput amplicon sequencing analysis indicated that water content, temperature, and pesticides had domain-specific effects on the diversity and taxonomic composition of bacterial, fungal, and protistan communities. Soil physicochemical properties had a more significant effect than pesticides on the various microbial domains in the vineyard soil. However, pesticide exposure emerged as a secondary factor explaining the variations in microbial communities, with a more substantial effect on protists compared to bacterial and fungal communities. Overall, our results highlight the variability in the dissipation kinetics and processes of pesticides in a multi-contaminated vineyard soil, as well as their effects on bacterial, fungal, and protistan communities.

Soil Characteristics Constrain the Response of Microbial Communities and Associated Hydrocarbon Degradation Genes during Phytoremediation.

Rhizodegradation is a promising cleanup technology where microorganisms degrade soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur between plant roots and soil microorganisms in contaminated soils that enhances natural microbial degradation. However, little is known about how different initial microbiotas influence the rhizodegradation outcome. Recent studies have hinted that soil initial diversity has a determining effect on the outcome of contaminant degradation. To test this, we either planted (P) or not (NP) balsam poplars (Populus balsamifera) in two soils of contrasting diversity (agricultural and forest) that were contaminated or not with 50 mg kg-1 of phenanthrene (PHE). The DNA from the rhizosphere of the P and the bulk soil of the NP pots was extracted and the bacterial genes encoding the 16S rRNA, the PAH ring-hydroxylating dioxygenase alpha subunits (PAH-RHDα) of Gram-positive and Gram-negative bacteria, and the fungal ITS region were sequenced to characterize the microbial communities. The abundances of the PAH-RHDα genes were quantified by real-time quantitative PCR. Plant presence had a significant effect on PHE degradation only in the forest soil, whereas both NP and P agricultural soils degraded the same amount of PHE. Fungal communities were mainly affected by plant presence, whereas bacterial communities were principally affected by the soil type, and upon contamination the dominant PAH-degrading community was similarly constrained by soil type. Our results highlight the crucial importance of soil microbial and physicochemical characteristics in the outcome of rhizoremediation.IMPORTANCE Polycyclic aromatic hydrocarbons (PAH) are a group of organic contaminants that pose a risk to ecosystems' health. Phytoremediation is a promising biotechnology with the potential to restore PAH-contaminated soils. However, some limitations prevent it from becoming the remediation technology of reference, despite being environmentally friendlier than mainstream physicochemical alternatives. Recent reports suggest that the original soil microbial diversity is the key to harnessing the potential of phytoremediation. Therefore, this study focused on determining the effect of two different soil types in the fate of phenanthrene (a polycyclic aromatic hydrocarbon) under balsam poplar remediation. Poplar increased the degradation of phenanthrene in forest, but not in agricultural soil. The fungi were affected by poplars, whereas total bacteria and specific PAH-degrading bacteria were constrained by soil type, leading to different degradation patterns between soils. These results highlight the importance of performing preliminary microbiological studies of contaminated soils to determine whether plant presence could improve remediation rates or not.

Body size determines soil community assembly in a tropical forest.

Tropical forests shelter an unparalleled biological diversity. The relative influence of environmental selection (i.e., abiotic conditions, biotic interactions) and stochastic-distance-dependent neutral processes (i.e., demography, dispersal) in shaping communities has been extensively studied for various organisms, but has rarely been explored across a large range of body sizes, in particular in soil environments. We built a detailed census of the whole soil biota in a 12-ha tropical forest plot using soil DNA metabarcoding. We show that the distribution of 19 taxonomic groups (ranging from microbes to mesofauna) is primarily stochastic, suggesting that neutral processes are prominent drivers of the assembly of these communities at this scale. We also identify aluminium, topography and plant species identity as weak, yet significant drivers of soil richness and community composition of bacteria, protists and to a lesser extent fungi. Finally, we show that body size, which determines the scale at which an organism perceives its environment, predicted the community assembly across taxonomic groups, with soil mesofauna assemblages being more stochastic than microbial ones. These results suggest that the relative contribution of neutral processes and environmental selection to community assembly directly depends on body size. Body size is hence an important determinant of community assembly rules at the scale of the ecological community in tropical soils and should be accounted for in spatial models of tropical soil food webs.

Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands.

The effect of plant species composition on soil microbial communities was studied at the multiregional level. We compared the soil microbial communities of alpine natural grasslands dominated by Carex curvula and anthropogenic subalpine pastures dominated by Nardus stricta. We conducted paired sampling across the Carpathians and the Alps and used Illumina sequencing to reveal the molecular diversity of soil microbes. We found that bacterial and fungal communities exhibited contrasting regional distributions and that the distribution in each grassland is well discriminated. Beta diversity of microbial communities was much higher in C. curvula grasslands due to a marked regional effect. The composition of grassland-type core microbiomes suggest that C. curvula, and N. stricta to a lesser extent, tend to select a cohort of microbes related to antibiosis/exclusion, pathogenesis and endophytism. We discuss these findings in light of the postglacial history of the studied grasslands, the habitat connectivity and the disturbance regimes. Human-induced disturbance in the subalpine belt of European mountains has led to homogeneous soil microbial communities at large biogeographical scales. Our results confirm the overarching role of the dominant grassland plant species in the distribution of microbial communities and highlight the relevance of biogeographical history.

Molecular diversity of Pseudoscorpiones in southern High Appalachian leaf litter.

The Pseudoscorpiones fauna of North America is diverse, but in regions like the southern Appalachian Mountains, they are still poorly documented with respect to their species diversity, distributions and ecology. Several families have been reported from these mountains and neighbouring areas. Here we analyse barcoding data of 136 specimens collected in leaf litter, most of them from high-elevation coniferous forest. We used ASAP as a species delimitation method to obtain an estimation of the number of species present in the region. For this and based on interspecific genetic distance values previously reported in Pseudoscorpions, we considered three different genetic Kimura two-parameter distance thresholds (3%/5%/8%), to produce more or less conservative estimates. These distance thresholds resulted in 64/47/27 distinct potential species representing the families Chthoniidae (33/22/12 species) and Neobisiidae (31/25/15) and at least six different genera within them. The diversity pattern seems to be affected by the Asheville Depression, a major biogeographic barrier in this area, with a higher diversity to the west of this geographic feature, particularly within the family Neobisiidae. The absence of representatives from other families amongst our studied samples may be explained by differences in their ecological requirements and occupation of different microhabitats.

Effect of Soil Type on Native Pterocypsela laciniata Performance under Single Invasion and Co-Invasion.

Native and invasive plant competition is usually controlled by the soil properties and the soil type underlying interspecific interactions. However, many uncertainties exist regarding the impact of soil type on native plant growth under single invasion and co-invasion despite the significant number of previous studies that focused on plant invasion. This study aims to elucidate the effects of soil type on the response of the native plant Pterocypsela laciniata under single invasion and co-invasion. Three different soils were used: natural soil, nutrient soil, and nutrient sterilized soil. The native P. laciniata was grown in monoculture and under single invasion and co-invasion with Solidago canadensis and Aster subulatus Michx. The results show that the native plant height and total biomass were 75% and 93.33% higher, respectively, in nutrient sterilized soil in monoculture than in natural and nutrient soil. In contrast, the native P. laciniata presents its best competitive ability in nutrient sterilized soil, being about 100% higher than in natural and nutrient soil under single invasion and co-invasion. However, no significant increase was observed in its growth parameters under co-invasion compared to single invasion. Conclusively, this study shows that nutrient soil sterilization positively affects native plant growth in monoculture and under single invasion, contrasting co-invasion in which more pronounced negative effects were observed on the native plant response.

Grapevine rootstock and soil microbiome interactions: Keys for a resilient viticulture.

Soil microbiota has increasingly been shown to play an integral role in viticulture resilience. The emergence of new metagenomic and culturomic technologies has led to significant advances in the study of microbial biodiversity. In the agricultural sector, soil and plant microbiomes have been found to significantly improve resistance to environmental stressors and diseases, as well as influencing crop yields and fruit quality thus improving sustainability under shifting environments. Grapevines are usually cultivated as a scion grafted on rootstocks, which are selected according to pedoclimatic conditions and cultural practices, known as terroir. The rootstock connects the surrounding soil to the vine's aerial part and impacts scion growth and berry quality. Understanding rootstock and soil microbiome dynamics is a relevant and important field of study, which may be critical to improve viticulture sustainability and resilience. This review aims to highlight the relationship between grapevine roots and telluric microbiota diversity and activity. In addition, this review explores the concept of core microbiome regarding potential applications of soil microbiome engineering with the goal of enhancing grapevine adaptation to biotic and abiotic stress.

High-Throughput Sequencing Analysis of the Composition and Diversity of the Bacterial Community in Cinnamomum camphora Soil.

Soil bacterial communities and root-associated microbiomes play important roles in the nutrient absorption and healthy growth of host plants. Cinnamomum camphora is an important timber and special economic forest tree species in Fujian Province. In this study, the high-throughput sequencing technique was used to analyze the composition, diversity, and function of the bacterial communities present in the soil from different samples and slope positions of C. camphora. The results of this analysis demonstrated that the related bacterial communities in C. camphora soil were mainly clustered based on sample type. Bacterial alpha diversity in the rhizosphere and bulk soil of C. camphora growing downhill was higher than that of C. camphora growing uphill. At the phylum level, Bacteroidetes, Proteobacteria, Chloroflexi, and Gemmatimonadetes were positively correlated with pH, available phosphorus, total phosphorus, available potassium, and total potassium, while Acidobacteria and Verrucomicrobia were negatively correlated with alkaline-hydrolyzable nitrogen. These results show that there were remarkable differences in the composition, diversity, and function of related bacterial communities between different sample types of C. camphora soil. The slope position had a marked effect on the bacterial communities in the rhizosphere and bulk soil, while the root endosphere remained unaffected.

Highly decomposed organic carbon mediates the assembly of soil communities with traits for the biodegradation of chlorinated pollutants.

To improve biodegradation strategies for chlorinated pollutants, the roles of soil organic matter and microbial function need to be clarified. It was hypothesised that microbial degradation of specific organic fractions in soils enhance community metabolic capability to degrade chlorinated pollutants. This field study used historic records of dieldrin concentrations since 1988 and established relationships between dieldrin dissipation and soil carbon fractions together with bacterial and fungal diversity in surface soils of Kurosol and Chromosol. Sparse partial least squares analysis linked dieldrin dissipation to metabolic activities associated with the highly decomposed carbon fraction. Dieldrin dissipation, after three decades of natural attenuation, was associated with increased bacterial species fitness for the decomposition of recalcitrant carbon substrates including synthetic chlorinated pollutants. These metabolic capabilities were linked to the decomposed carbon fraction, an important driver for the microbial community and function. Common bacterial traits among taxonomic groups enriched in samples with high dieldrin dissipation included their slow growth, large genome and complex metabolism which supported the notion that metabolic strategies for dieldrin degradation evolved in an energy-low soil environment. The findings provide new perspectives for bioremediation strategies and suggest that soil management should aim at stimulating metabolism at the decomposed, fine carbon fraction.

Composition of soil organic matter drives total loss of dieldrin and dichlorodiphenyltrichloroethane in high-value pastures over thirty years.

The residues of dieldrin and dichlorodiphenyltrichloroethane (DDT), internationally-banned agricultural insecticides, continue to exceed government guidelines in some surface soils 30 years after use. Little is known regarding the soil factors and microbial community dynamics associated with the in-situ biodegradation of these organochlorine chemicals. We hypothesised that soil organic matter, a key factor affecting microbial biomass and diversity, affects the biodegradation and total loss of the pollutants 30 years after use. We sampled 12 contaminated paddocks with residue concentrations monitoring data since 1988 that represent two different agricultural surface-soils. The total loss and current concentrations of the residues was correlated with soil physicochemical properties, microbial biomass carbon, microbial community diversity indices and microbial community abundance. Current dieldrin and DDT residue concentrations were positively correlated with soil organic matter and clay contents. However, key indicators for loss of residues after 23-30 years were low carbon-to­nitrogen ratios, high microbial-C-to-total-C ratios and high fungal community evenness. The results support the composition of soil organic matter as an important factor affecting degradation of organochlorines and that co-metabolism of dieldrin and DDT could be enhanced by manipulating the composition of soil organic matter to cater for a broad diversity of microbial function.