Soil microbial communities in restored and unrestored coastal dune ecosystems in California

Most restoration projects involving invasive plant eradication tend to focus on plant removal with little consideration given to how these invasives change soil microbial communities. However, soil microorganisms can determine invasibility of habitats and, in turn, be altered by invasives once established, potentially inhibiting native plant establishment. We studied soil microbial communities in coastal dunes with varying invasion intensity and different restoration approaches (herbicide, mechanical excavation) at Point Reyes National Seashore. Overall, we found evidence of a strong link between bacterial and fungal soil communities and the presence of invasives and restoration approach. Heavily invaded sites were characterized by a lower abundance of putatively identified nitrifiers, fermentative bacteria, fungal parasites, and fungal dung saprotrophs and a higher abundance of cellulolytic bacteria and a class of arbuscular mycorrhizal fungi (Archaeosporomycetes). Changes in soil microbiota did not fully dissipate following removal of invasives using herbicide, with exception of reductions in cellulolytic bacteria and Archaeosporomycetes abundance. Mechanical restoration effectively removed both invasives and soil legacy effects by inverting or “flipping” rhizome-contaminated surface soils with soils from below and may have inadvertently induced other adverse effects on soils that impeded reestablishment of native dune plants. Land managers should consider additional measures to counteract lingering legacy effects and/or focus restoration efforts in areas where legacy effects are less pronounced

Native and invasive inoculation sources modify fungal community assembly and biomass production of a chaparral shrub

Feedbacks between plants and surrounding soil microbes can contribute to the establishment and persistence of invasive annual grasses as well as limit the success of restoration efforts. In this study, we aim to understand how three sources of soil inocula – native, invasive (from under Bromus diandrus) and sterile – affect the growth response and fungal community composition in the roots of a chaparral shrub, Adenostoma fasciculatum. We grew A. fasciculatum from seed in a greenhouse with each inoculum source and harvested at six months. We measured above- and below-ground biomass, arbuscular mycorrhizal fungal (AMF) colonization and conducted targeted-amplicon sequencing of the 18S and ITS2 loci to characterize AMF and general fungal community composition, respectively. Native inoculum resulted in roots with richer communities of some groups of AMF and non-AMF symbionts, when compared to roots grown with invasive or sterile inoculum. Seedlings grown with invasive and native inoculum did not have different growth responses, but both produced more biomass than a sterile control. These findings suggest that inoculation with soil from native species can increase the diversity of multiple groups of fungal symbionts and inoculation with live soil (invasive or native) can increase seedling biomass. Moreover, future work would benefit from assessing if a more diverse community of fungal symbionts increases seedling survival when planted in field restoration sites

Effects of compost application on soil macrofauna and soil functions in oil palm plantation – Biofunctool® approach

Oil palm produces about 38.7% of all vegetable oil (palm oil and palm kernel oil, 2016) and its cultivation area reach in 18.7 million ha worldwide (mature plantations) in 2017. While palm oil demand will increase in the future, leading an increase of global production, an adapted fertilization is needed to increase yield while preserving soil multifunctionality. Organic fertilization, by Empty fruit bunches (EFB) or compost is an alternative to mineral fertilization. The effect of EFB application on soil quality has been investigated, however the effect of compost application on soil functions and soil macrofauna in oil palm plantations is poorly known. To investigate the effect of compost application, we compared soil functions and soil macrofauna of two treatments of an agronomical trial (compost application / mineral fertilization), taking into account the zone around the palm tree (harvesting path, circle and windrow). Soil functions were assessed using the Biofunctool® framework, which is a novel set of in-field, low tech and time-effective indicators to assess main soil functions: soil carbon transformation, nutrient cycling and structure maintenance. Effect of the zone around the palm tree on soil functions and macrofauna, was largest than the effect of the treatment and the compost application slightly improved carbon transformation functions in the circle zone. Soil functions and macrofauna functional groups data showed similar co-structures indicating the link between soil functions and fauna. We highlighted the importance of spatial heterogeneity and discussed the effect of organic matter

Impacts of farming practice within organic farming systems on below-ground ecology and ecosystem function

Maintaining ecosystem function is a key issue for sustainable farming systems which contribute broadly to global ecosystem health. A focus simply on the diversity of belowground organisms is not sufficient and there is a need to consider the contribution of below-ground biological processes to the maintenance and enhancement of soil function and ecosystem services. A critical literature review on the impacts of land management practices on below-ground ecology and function shows that farm management practices can have a major impact. A particular challenge for organic farming systems is to explore to what extent reduced tillage can be adopted to the benefit of below-ground ecology without critically upsetting the whole farm management balance

A review of the influence of root-associating fungi and root exudates on the success of invasive plants

Plant-fungal interactions are essential for understanding the distribution and abundance of plants species. Recently, arbuscular mycorrhizal fungal (AMF) partners of non-indigenous invasive plants have been hypothesized to be a critical factor influencing the invasion processes. AMF are known to improve nutrient and moisture uptake, as well as disrupt parasitic and pathogenic microbes in the host plant. Such benefits may enable invaders to establish significant and persistent populations in environments previously dominated by natives. Coupling these findings with studies on invader pathogen-disrupting root exudates is not well documented in the literature describing plant invasion strategies. The interaction effects of altered AMF associations and the impact of invader root exudates would be more relevant than understanding the AMF dynamics or the phytochemistry of successful invaders in isolation, particularly given that AMF and root exudates can have a similar role in pathogen control but function quite differently. One means to achieve this goal is to assess these strategies concurrently by characterizing both the general (mostly pathogens or commensals) and AM-specific fungal colonization patterns found in field collected root samples of successful invaders, native plants growing within dense patches of invaders, and native plants growing separately from invaders. In this review I examine the emerging evidence of the ways in which AMF-plant interactions and the production of defensive root exudates provide pathways to invasive plant establishment and expansion, and conclude that interaction studies must be pursued to achieve a more comprehensive understanding of successful plant invasion

Inter-plant communication through mycorrhizal networks mediates complex adaptive behaviour in plant communities

Adaptive behaviour of plants, including rapid changes in physiology, gene regulation and defence response, can be altered when linked to neighbouring plants by a mycorrhizal network (MN). Mechanisms underlying the behavioural changes include mycorrhizal fungal colonization by the MN or interplant communication via transfer of nutrients, defence signals or allelochemicals. We focus this review on our new findings in ectomycorrhizal ecosystems, and also review recent advances in arbuscular mycorrhizal systems. We have found that the behavioural changes in ectomycorrhizal plants depend on environmental cues, the identity of the plant neighbour and the characteristics of the MN. The hierarchical integration of this phenomenon with other biological networks at broader scales in forest ecosystems, and the consequences we have observed when it is interrupted, indicate that underground ‘tree talk’ is a foundational process in the complex adaptive nature of forest ecosystems

Biotechnology, environmental forcing, and unintended trophic cascades

A long ongoing discussion between scientists and policy decision-makers seems to have entered recently into a new phase. The consequences of release of transgenic crops into the environment are being discussed not only by scientists but also by farmers, environmental groups and politicians, while an increasing amount of data is becoming available at all biological scales, including the field level. However, data still rely on experiments designed to capture direct consumer¿resource interactions. Here we argue that we should attempt to concentrate on the ecosystem functioning of soil biota under genetically-modified (GM) plants, because functional and mechanistic analysis of the multitrophic effects of GM plants on soil biota is still lacking. It is our opinion that we should avoid addressing taxa and soil communities separately, but link them at their functional level. We shall explain why, using examples from ecosystem services, allometric scaling, and soil food webs. The energy flow of any food web under stress incorporates several factors and pooled information on ecosystem services and on the different responses of soil invertebrates to induced perturbations in other trophic levels. Therefore, we will systematically focus on the complementarities of these approache

Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition.

Mortierella and Ilyonectria genera include common species of soil fungi that are frequently detected as root endophytes in many plants, including Populus spp. However, the ecological roles of these and other endophytic fungi with respect to plant growth and function are still not well understood. The functional ecology of two key taxa from the P. trichocarpa rhizobiome, M. elongata PMI93 and I. europaea PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, M. elongata was observed to promote the growth of P. trichocarpa. This response was cultivar independent. In contrast, I. europaea had no visible effect on P. trichocarpa growth. Metatranscriptomic studies revealed that these fungi impacted rhizophytic and endophytic activities in P. trichocarpa and induced shifts in soil and root microbial communities. Differential expression of core genes in P. trichocarpa roots was observed in response to both fungal species. Expression of P. trichocarpa genes for lipid signaling and nutrient uptake were upregulated, and expression of genes associated with gibberellin signaling were altered in plants inoculated with M. elongata, but not I. europaea. Upregulation of genes for growth promotion, downregulation of genes for several leucine-rich repeat receptor kinases, and alteration of expression of genes associated with plant defense responses (e.g., jasmonic acid, salicylic acid, and ethylene signal pathways) also suggest that M. elongata manipulates plant defenses while promoting plant growth

Tree invasions and biosecurity: eco-evolutionary dynamics of hitchhiking fungi

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