Complete Genome Sequence of Achromobacter Strain ES-001, a Betaproteobacterium Associated with a Cellulolytic Soil Community

The genome sequence of the soilborne bacterium Achromobacter strain ES-001, assembled from Illumina NextSeq and Nanopore MinION reads, is rich in genes predicted to encode iron, arsenic, and hydrocarbon metabolism, as well as type 6 secretion components. The sequenced genome will aid in determining the roles of noncellulolytic species in cellulose-enriched environments.

Foliar Aphid Herbivory Alters the Tomato Rhizosphere Microbiome, but Initial Soil Community Determines the Legacy Effects

Aboveground herbivory can impact the root-associated microbiome, while simultaneously different soil microbial communities influence herbivore performance. It is currently unclear how these reciprocal top-down and bottom-up interactions between plants, insects and microbes vary across different soils and over successive plant generations. In this study, we examined top-down impacts of above-ground herbivory on the rhizosphere microbiome across different soils, assessed bottom-up impacts of soil microbial community variation on herbivore performance, and evaluated their respective contributions to soil legacy effects on herbivore performance. We used Macrosiphum euphorbiae (potato aphid) and Solanum pimpinellifolium (wild tomato) to capture pre-domestication microbiome interactions with a specialist pest. First, using 16S rRNA sequencing we compared bacterial communities associated with rhizospheres of aphid-infested and uninfested control plants grown in three different soils over three time points. High aphid infestation impacted rhizosphere bacterial diversity in a soil-dependent manner, ranging from a 22% decrease to a 21% increase relative to uninfested plants and explained 6–7% of community composition differences in two of three soils. We next investigated bottom-up and soil legacy effects of aphid herbivory by growing wild tomatoes in each of the three soils and a sterilized “no microbiome” soil, infesting with aphids (phase one), then planting a second generation (phase two) of plants in the soil conditioned with aphid-infested or uninfested control plants. In the first phase, aphid performance varied across plants grown in different soil sources, ranging from a 20 to 50% increase in aphid performance compared to the “no microbiome” control soil, demonstrating a bottom-up role for soil microbial community. In the second phase, initial soil community, but not previous aphid infestation, impacted aphid performance on plants. Thus, while herbivory altered the rhizosphere microbiome in a soil community-dependent manner, the bottom-up interaction between the microbial community and the plant, not top-down effects of prior herbivore infestation, affected herbivore performance in the following plant generation. These findings suggest that the bottom-up effects of the soil microbial community play an overriding role in herbivore performance in both current and future plant generations and thus are an important target for sustainable control of herbivory in agroecosystems.

Fungi play a key role in the restoration of species-rich grasslands: trace-labelling carbon through the food chain

<p>Restoring natural plant communities on abandoned agricultural fields can be challenging due to a degraded soil community and a fertilizer legacy. We discovered that fungi are the initiators of a tighter connected soil food web which restores the closed carbon and nutrients cycles in soils, thereby accommodating species-rich plant communities in grasslands. Boosting the fungal channel as a bottom-up approach could thus be used as a next-generation restoration measure. We show data of soil inoculation experiments and trace the progression of change in the fungal community via sequencing and functioning via community response profiles. We assessed the top-down foraging of predators and consumers on the microbiome by analysing gut contents of consumers and predators from different restoration stages. We will be able to show preliminary data on the effect of fungi and their higher trophic levels in stimulating species-rich plant communities as well as give a prospect on the wider applications for microbiome engineering.</p>

Soil biota and non-native plant invasions.

The trajectory of plant invasions - for better or for worse - can be tied to interactions between plants and the soil community. Here, we highlight five broad ways in which belowground interactions can influence the trajectory of biological invasions by non-native plant species. First, many non-native plant species in their non-native ranges can interact very differently with the resident soil community than do native species. Second, non-native plant species often interact very differently with the soil community in their non-native ranges than in their native ranges, which can result in enemy release from antagonistic interactions. Third, non-native plant species can cultivate a soil community that disproportionately harms native competitors in invaded communities. Fourth, antagonistic soil biota in invaded communities can reduce the performance of non-native plant species, resulting in meaningful biotic resistance against invasion. Fifth, besides or in addition to antagonistic interactions with soil biota, soil mutualisms can promote the success of invasive plant species (i) when mutualists co-invade with non-native plant species that require obligate specialist mutualists, (ii) when mutualists enhance the performance of non-native plant species in their non-native ranges, and (iii) when biotic interactions in the invaded community suppress the soil mutualists of native plant species. We conclude that management practices aimed at manipulating plant - soil interactions have considerable potential to help control plant invasions, but further work is needed to understand the spatial, temporal, taxonomic and biogeographic drivers of context dependence in interactions among plants and soil biota.

Plant diversity effects on herbivory are mediated by soil biodiversity and plant chemistry

Insect herbivory is a key process in ecosystem functioning. While theory predicts that plant diversity modulates herbivory, the mechanistic links remain unclear. We postulated that the plant metabolome mechanistically links plant diversity and herbivory. In autumn and in spring, we assessed aboveground herbivory rates and plant metabolomes of seven plant species in experimental plant communities varying in plant species and resource acquisition strategy diversity. In the same plots, we also measured plant individual biomass as well as soil microbial and nematode community composition. Herbivory rates decreased with increasing plant species richness. Path modelling revealed that plant species richness and community resource acquisition strategy affected soil community composition. In particular, changes in nematode community composition affected plant metabolomes and thereby herbivory rates. These results provide experimental evidence that soil community composition plays an important role in reducing herbivory rates with increasing plant diversity by changing plant metabolomes.

Metagenomic analysis reveals rapid development of soil biota on fresh volcanic ash

Little is known of the earliest stages of soil biota development of volcanic ash, and how rapidly it can proceed. We investigated the potential for soil biota development during the first 3 years, using outdoor mesocosms of sterile, freshly fallen volcanic ash from the Sakurajima volcano, Japan. Mesocosms were positioned in a range of climates across Japan and compared over 3 years, against the developed soils of surrounding natural ecosystems. DNA was extracted from mesocosms and community composition assessed using 16S rRNA gene sequences. Metagenome sequences were obtained using shotgun metagenome sequencing. While at 12 months there was insufficient DNA for sequencing, by 24 months and 36 months, the ash-soil metagenomes already showed a similar diversity of functional genes to the developed soils, with a similar range of functions. In a surprising contrast with our hypotheses, we found that the developing ash-soil community already showed a similar gene function diversity, phylum diversity and overall relative abundances of kingdoms of life when compared to developed forest soils. The ash mesocosms also did not show any increased relative abundance of genes associated with autotrophy (rbc, coxL), nor increased relative abundance of genes that are associated with acquisition of nutrients from abiotic sources (nifH). Although gene identities and taxonomic affinities in the developing ash-soils are to some extent distinct from the natural vegetation soils, it is surprising that so many of the key components of a soil community develop already by the 24-month stage. In this system, however, rapid development may be facilitated by the relatively moderate pH of the Sakurajima ash, proximity of our mesocosms to propagule sources, and the rapid establishment of a productive bryophyte and lichen layer on the surface. Ash from other volcanoes richer in acids or more distant from propagule sources could show a different pattern and slower soil biota development.

The ‘fertile island effect’ of Welwitschia plants on soil microbiota is influenced by plant gender

ABSTRACT Desert and semi-desert plants are often associated with a distinct soil biota under the plants and close to the root system. We aimed to understand if similar effects could be found in the taxonomically isolated desert gymnosperm Welwitschia mirabilis in the Namib Desert, and whether this island effect varied with climate and with gender of plants. We took soil cores adjacent to the plants in environments ranging from extreme desert to arid shrubland, and in nearby control sites between the plants. Soil chemistry was analysed, and deoxyribonucleic acid was extracted and sequenced for the bacterial 16s region. Soil under the plants was richer in organic C, N and moisture. Despite the range of climates, the soil around Welwitschia plants was consistently associated with a particular bacterial community composition that was distinct from samples further away. Compared to unvegetated control patches, bacterial diversity close to the plants was reduced. In the plant-associated soil community, there was a clear gender effect across all sites with a distinct community composition and greater diversity under male plants. It is unclear what differences in the soil environment might be producing these gender-associated differences, which provide an additional dimension to the fertile island effect.

Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment

Microplastics are recognized as an emerging contaminant worldwide. Although microplastics have been shown to strongly affect organisms in aquatic environments, less is known about whether and how microplastics can affect different taxa within a soil community, and it is unclear whether these effects can cascade through soil food webs. By conducting a microplastic manipulation experiment, i.e. adding low-density polyethylene fragments in the field, we found that microplastic addition significantly affected the composition and abundance of microarthropod and nematode communities. Contrary to soil fauna, we found only small effects of microplastics on the biomass and structure of soil microbial communities. Nevertheless, structural equation modelling revealed that the effects of microplastics strongly cascade through the soil food webs, leading to the modification of microbial functioning with further potential consequences on soil carbon and nutrient cycling. Our results highlight that taking into account the effects of microplastics at different trophic levels is important to elucidate the mechanisms underlying the ecological impacts of microplastic pollution on soil functioning.