Biological soil crusts on agricultural soils of mesic regions promote microbial cross-kingdom co-occurrences and nutrient retention

Introduction

Biological soil crusts (biocrusts) are known as biological hotspots on undisturbed, nutrient-poor bare soil surfaces and until now, are mostly observed in (semi-) arid regions but are currently poorly understood in agricultural systems. This is a crucial knowledge gap because managed sites of mesic regions can quickly cover large areas. Thus, we addressed the questions (i) if biocrusts from agricultural sites of mesic regions also increase nutrients and microbial biomass as their (semi-) arid counterparts, and (ii) how microbial community assemblage in those biocrusts is influenced by disturbances like different fertilization and tillage regimes.

Methods

We compared phototrophic biomass, nutrient concentrations as well as the abundance, diversity and co-occurrence of Archaea, Bacteria, and Fungi in biocrusts and bare soils at a site with low agricultural soil quality.

Results and Discussion

Biocrusts built up significant quantities of phototrophic and microbial biomass and stored more nutrients compared to bare soils independent of the fertilizer applied and the tillage management. Surprisingly, particularly low abundant Actinobacteria were highly connected in the networks of biocrusts. In contrast, Cyanobacteria were rarely connected, which indicates reduced importance within the microbial community of the biocrusts. However, in bare soil networks, Cyanobacteria were the most connected bacterial group and, hence, might play a role in early biocrust formation due to their ability to, e.g., fix nitrogen and thus induce hotspot-like properties. The microbial community composition differed and network complexity was reduced by conventional tillage. Mineral and organic fertilizers led to networks that are more complex with a higher percentage of positive correlations favoring microbe-microbe interactions. Our study demonstrates that biocrusts represent a microbial hotspot on soil surfaces under agricultural use, which may have important implications for sustainable management of such soils in the future.

Post-reclamation microbial diversity and functions in hexachlorocyclohexane (HCH) contaminated soil in relation to spontaneous HCH tolerant vegetation

The toxicity, volatility and persistence of the obsolete organochlorine pesticide hexachlorocyclohexane (HCH), makes reclamation of contaminated areas a priority for the health and welfare of neighboring human communities. Microbial diversity and functions and their relation to spontaneous vegetation in post-excavation situations, are essential indicators to consider in bioaugmentation or microbe-assisted phytoremediation strategies at field scale. Our study aimed to evaluate the effects of long-term HCH contamination on soil and plant-associated microbial communities, and whether contaminated soil has the potential to act as a bacterial inoculum in post-excavation bioremediation strategies. To scrutinize the role of vegetation, the potential nitrogen fixation of free-living and symbiotic diazotrophs of the legume Lotus tenuis was assessed as a measure of nutrient cycling functions in soil under HCH contamination. Potential nitrogen fixation was generally not affected by HCH, with the exception of lower nifH gene counts in excavated contaminated rhizospheres, most probably a short-term HCH effect on early bacterial succession in this compartment. HCH shaped microbial communities in long-term contaminated bulk soil, where we identified possible HCH tolerants such as Sphingomonas and Altererythrobacter. In L. tenuis rhizosphere, microbial community composition was additionally influenced by plant growth stage. Sphingobium and Massilia were the bacterial genera characteristic for HCH contaminated rhizospheres. Long-term HCH contamination negatively affected L. tenuis growth and development. However, root-associated bacterial community composition was driven solely by plant age, with negligible HCH effect. Results showed that L. tenuis acquired possible HCH tolerant bacteria such as the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade, Sphingomonas, Massilia or Pantoea which could simultaneously offer plant growth promoting (PGP) benefits for the host. Finally, we identified an inoculum with possibly HCH tolerant, PGP bacteria transferred from the contaminated bulk soil to L. tenuis roots through the rhizosphere compartment, consisting of Mesorhizobium loti, Neorhizobium galegae, Novosphingobium lindaniclasticum, Pantoea agglomerans and Lysobacter bugurensis.

52 years of ecological restoration following a major disturbance by opencast lignite mining does not reassemble microbiome structures of the original arable soils

Opencast mining for lignite continuously creates areas of land that require restoration. Here we applied a chronosequence approach to investigate the development of soil bacterial communities during 52 years as influenced by the restoration process and subsequent changes in soil physico-chemical conditions starting from the initial reclamation of the sites. By comparison with the unaffected soils near the mine, we were able to address the question if soil bacterial communities have reached a steady state within 52 years, which is comparable to the original soil. Our study revealed three distinct phases of the restoration process, each with a specific bacterial community composition. The effect size of these changes was similar to the one observed for seasonal dynamics at our sites. At the beginning of the restoration process Flavobacteriaceae, Cytophagaceae and Sphingobacteriaceae were found as typical members of the bacterial community as well as Rhizobiales as a result of the cultivation of alfalfa on the restored plots. At later stage the families Peptostreptococcaceae, Desulfurellaceae as well as Streptomycetaceae increased in relative abundance and became dominant members of the bacterial community. Even though overall bacterial abundance and richness exhibited values comparable to the original soil already 5 years after the start of the restoration process, main responder analyses reveal differences in the bacterial community structure even 52 years after the start of the restoration process. Mostly Nitrospirae were reduced in abundance in the soils restored for 52 years compared to the original soils. To broaden the significance of our study, we compared our data bioinformatically with published results from other restored areas, which were previously affected by opencast mining. Despite different durations of the different restoration phase, we could observe a large degree of conformity when bacterial patterns of succession were compared indicating common modes of action of ecological restoration tools for bacterial communities.

Under temperate climate, the conversion of grassland to arable land affects soil nutrient stocks and bacteria in a short term

Projected population growth and climate change will make it inevitable to convert neglected and marginal land into productive arable land. We investigate the influence of agricultural management practices on nutrient stocks and soil functions during the conversion of former extensively used grassland to arable land. Effects of grassland removal, tillage, intercropping with faba bean (Vicia faba) and its later incorporation were studied with respect to soil properties and bacterial community structure. Therefore, composite samples were collected with a core sampler from the topsoil (0-20 cm) in (a) the initial grassland, (b) the transitional phase during the vegetation period of V. faba, (c) after ploughing the legume in, and (d) untreated controls. In all samples, nitrate-N, ammonium-N, dissolved organic carbon (DOC) and total nitrogen bound (TNb) were analyzed and comparisons of the bacterial community structure after 16S-amplicon sequencing were performed to assess soil functions. Mineralization after grassland conversion followed by the biological nitrogen fixation of broad beans enhanced the nitrate-N content in bulk soil from 4 to almost 50 μg N g^-1dw. Bacterial community structure on phylum level in bulk soil was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes and remained almost stable. However, alpha and beta-diversity analysis revealed a change of the bacterial composition at the final state of the conversion. This change was primarily driven by increasing abundances of the genera Massilia and Lysobacter, both members of the Proteobacteria, after the decay of the leguminous plant residues. Furthermore, increasing abundances of the family Gaiellaceae and its genus Gaiella fostered this change and were related to the decreasing carbon to nitrogen ratio. In short, gentle management strategies could replace the input of mineral fertilizer with the aim to contribute to future sustainable and intensified production even on converted grassland.

HCH phytoremediation potential of native plant species from a contaminated urban site in Turda, Romania

Current physical or chemical methods used for remediation of soils contaminated with hexachlocyclohexane (HCH), leave behind significant levels of pollutants. Given the compound's volatility and persistence in the environment, sites contaminated with HCH remain a concern for the population living in nearby areas. By making use of both the recovery capacity and the pollutant uptake ability of spontaneously growing vegetation, our study aimed to identify native plant species able to cover and moreover take up the HCH left at a former lindane production unit in Turda, Romania. The results showed that dominant species across the study site like Lotus tenuis, Artemisia vulgaris or Tanacetum vulgare, were capable of taking up HCH in their tissues, according to different patterns that combined at the scale of the plant community. Regardless of the proximity of the HCH contamination hotspots, the development of the plant cover was characteristic for vegetation succession on disturbed soils of the Central European region. Finally, we conclude that plant species which grow spontaneously at the HCH contaminated site in Turda and are capable of taking up the pollutant, represent a self-sustainable and low maintenance phytomanagement approach that would allow for the reintegration of the site in the urban or industrial circuit and nevertheless would reduce the toxicity risk to the neighboring human inhabitants.

Organic Amendments in a Long-term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis

This study intended to elucidate the long-term effects of organic soil amendments on bacterial co-occurrence in bulk soil with and without addition of mineral fertiliser. Previous research mostly neglected the bacterial co-occurrence structure and focussed mainly on the parameters species diversity and abundance changes of species. Here we present a systematic comparison of two frequently used soil amendments, manure and straw, with regard to their impact on bacterial co-occurrence in a long-term field trial in Speyer, Germany. The approach involved 16S amplicon sequencing in combination with a bacterial network analysis, comparing the different fertiliser regimes. The results show an increase of bacterial diversity as well as an accumulation of bacteria of the order Bacillales in plots fertilised with manure compared to a control treatment. In the straw-amended plots neither an increase in diversity was found nor were indicative species detectable. Furthermore, network analysis revealed a clear impact of mineral fertiliser addition on bacterial co-occurrence structure. Most importantly, both organic amendments increased network complexity irrespective of mineral fertilisation regime. At the same time, the effects of manure and straw exhibited differences that might be explained by differences in their nutritional/chemical contents. It is concluded that bacterial interactions are a crucial parameter for the assessment of amendment effects regarding soil health and sustainability.