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

Practical applications of soil microbiota to improve ecosystem restoration: current knowledge and future directions

Soil microbiota are important components of healthy ecosystems. Greater consideration of soil microbiota in the restoration of biodiverse, functional, and resilient ecosystems is required to address the twin global crises of biodiversity decline and climate change. In this review, we discuss available and emerging practical applications of soil microbiota into (i) restoration planning, (ii) direct interventions for shaping soil biodiversity, and (iii) strategies for monitoring and predicting restoration trajectories. We show how better planning of restoration activities to account for soil microbiota can help improve progress towards restoration targets. We show how planning to embed soil microbiota experiments into restoration projects will permit a more rigorous assessment of the effectiveness of different restoration methods, especially when complemented by statistical modelling approaches that capitalise on existing data sets to improve causal understandings and prioritise research strategies where appropriate. In addition to recovering belowground microbiota, restoration strategies that include soil microbiota can improve the resilience of whole ecosystems. Fundamentally, restoration planning should identify appropriate reference target ecosystem attributes and - from the perspective of soil microbiota - comprehensibly consider potential physical, chemical and biological influences on recovery. We identify that inoculating ecologically appropriate soil microbiota into degraded environments can support a range of restoration interventions (e.g. targeted, broad-spectrum and cultured inoculations) with promising results. Such inoculations however are currently underutilised and knowledge gaps persist surrounding successful establishment in light of community dynamics, including priority effects and community coalescence. We show how the ecological trajectories of restoration sites can be assessed by characterising microbial diversity, composition, and functions in the soil. Ultimately, we highlight practical ways to apply the soil microbiota toolbox across the planning, intervention, and monitoring stages of ecosystem restoration and address persistent open questions at each stage. With continued collaborations between researchers and practitioners to address knowledge gaps, these approaches can improve current restoration practices and ecological outcomes.

Prairie restoration promotes the abundance and diversity of mutualistic arbuscular mycorrhizal fungi

Predicting how biological communities assemble in restored ecosystems can assist in conservation efforts, but most research has focused on plants, with relatively little attention paid to soil microbial organisms that plants interact with. Arbuscular mycorrhizal (AM) fungi are an ecologically significant functional group of soil microbes that form mutualistic symbioses with plants and could therefore respond positively to plant community restoration. To evaluate the effects of plant community restoration on AM fungi, we compared AM fungal abundance, species richness, and community composition of five annually cultivated, conventionally managed agricultural fields with paired adjacent retired agricultural fields that had undergone prairie restoration 5-9 years prior to sampling. We hypothesized that restoration stimulates AM fungal abundance and species richness, particularly for disturbance-sensitive taxa, and that gains of new taxa would not displace AM fungal species present prior to restoration due to legacy effects. AM fungal abundance was quantified by measuring soil spore density and root colonization. AM fungal species richness and community composition were determined in soils and plant roots using DNA high-throughput sequencing. Soil spore density was 2.3 times higher in restored prairies compared to agricultural fields, but AM fungal root colonization did not differ between land use types. AM fungal species richness was 2.7 and 1.4 times higher in restored prairies versus agricultural fields for soil and roots, respectively. The abundance of Glomeraceae, a disturbance-tolerant family, decreased by 25% from agricultural to restored prairie soils but did not differ in plant roots. The abundance of Claroideoglomeraceae and Diversisporaceae, both disturbance-sensitive families, was 4.6 and 3.2 times higher in restored prairie versus agricultural soils, respectively. Species turnover was higher than expected relative to a null model, indicating that AM fungal species were gained by replacement. Our findings demonstrate that restoration can promote a relatively rapid increase in the abundance and diversity of soil microbial communities that had been degraded by decades of intensive land use, and community compositional change can be predicted by the disturbance tolerance of soil microbial taxonomic and functional groups.

The Legacy of Plant Invasion: Impacts on Soil Nitrification and Management Implications

Plant invasions can have long-lasting impacts on soil nitrification, which plays a critical role in nutrient cycling and plant growth. This review examines the legacy effects of plant invasion on soil nitrification, focusing on the underlying mechanisms, context dependence, and implications for management. We synthesize literature on the positive, negative and neutral legacy effects of plant invasion on soil nitrification, highlighting the complexity of these effects and the need for further research to fully understand them. Positive legacy effects include increased soil microbial biomass or activity, potentially enhancing nutrient availability for plants. However, negative legacy effects, like reduced nitrifier abundance, can result in decreased soil nitrification rates and nutrient availability. In some cases, changes to nitrification during active invasion appear transitory after the removal of invasive plants, indicating neutral short-term legacies. We discuss the context dependence of legacy effects considering factors, including location, specific invasive plant species, and other environmental conditions. Furthermore, we discuss the implications of these legacy effects for management and restoration strategies, such as the removal or control of invasive plants, and potential approaches for restoring ecosystems with legacy effects on soil nitrification. Finally, we highlight future research directions, including further investigation into the mechanisms and context dependence of legacy effects, and the role of plant-microbe interactions. Overall, this review provides insights into the legacy effects of plant invasion on soil nitrification and their implications for ecosystems.

Plastic litter changes the rhizosphere bacterial community of coastal dune plants

The presence of plastic litter in coastal environments like beach-dune systems has been well documented, and recent studies have shown that this pollutant can influence sand properties as well as dune vegetation. However, the effects of plastics on rhizosphere bacterial communities of dune plants have largely been neglected. This is an ecologically relevant issue since these communities may play an important role in improving plant growth and resilience of dune systems. Here, we explored the impact of plastic litter made of either non-biodegradable polymers (NBP) or biodegradable/compostable polymers (BP) on the structure and composition of rhizosphere bacterial communities associated with two widespread species along coastal European dunes, Thinopyrum junceum and Sporobolus pumilus, by using a one-year field experiment combined with metabarcoding techniques. Both plastics did not affect neither the survival nor the biomass of T. junceum plants, but they significantly increased alpha-diversity of rhizosphere bacterial communities. They also changed rhizosphere composition by increasing the abundance of the phyla Acidobacteria, Chlamydiae, and Nitrospirae, and of the family Pirellulaceae, and reducing the abundance of the family Rhizobiaceae. NBP reduced drastically the survival of S. pumilus while BP increased its root biomass compared to controls. BP also increased the abundance of the phylum Patescibacteria of the rhizosphere bacterial communities. Our findings provide the first evidence that NBP and BP can change rhizosphere bacterial communities associated with dune plants and highlight the importance of investigating how these changes can affect the resilience of coastal dunes to climate change.

Nitrapyrin Addition Mitigated CO2 Emission from a Calcareous Soil Was Closely Associated with Its Effect on Decreasing Cellulolytic Fungal Community Diversity

Application of nitrification inhibitors (NIs) has been widely used to inhibit nitrification and reduce N₂O emissions. However, the impacts of NI addition on soil carbon transformation and carbon-degrading microbial communities have not been well explored. Here, a microcosm experiment was carried out, and four treatments were designed: (i) unfertilized control, (ii) urea alone, (iii) urea plus cattle manure, and (iv) urea plus cattle manure with nitrapyrin. The influence of nitrapyrin on soil CO₂ emissions, carbon-degrading extracellular enzyme activities, and the abundance and diversity of the cbhI community was investigated. Compared to the treatment of urea plus cattle manure, nitrapyrin significantly decreased cumulative CO₂ emissions by 51.8%. Moreover, cbhI community gene copies and their α-diversities (P < 0.05) were also significantly reduced by nitrapyrin application. A partial least squares path model showed that CO₂ emission was positively associated with cbhI community α-diversity but negatively associated with nitrapyrin addition. We conclude that the mitigation of soil CO₂ emissions by nitrapyrin can be ascribed to its effects on decreasing of cellulose-degrading gene community diversity. Our findings provide new insights into the side-effects of nitrapyrin on abating CO₂ emission.

Ammophila Invasion Ecology and Dune Restoration on the West Coast of North America

The invasive ecosystem engineer Ammophila arenaria, native to Europe, was first introduced to California (USA) in 1896. More than a century later, it has come to dominate coastal foredune vegetation on the west coast of North America to the near exclusion of native species. A. arenaria builds a narrow, steep, peaked, and densely vegetated foredune, in contrast to the broad, more sparsely vegetated foredunes built by the native Elymus mollis. As such, it has modified dune processes by fixing the foredune and disrupting exchange of sediment between the beach, foredune, and dunefield. In the 1930s the congener A. breviligulata, native to the east coast and Great Lakes USA, was first introduced to Oregon, and has been displacing A. arenaria in southern Washington. Ammophila spp. have drastically reduced biodiversity, outcompeting native plant species, and displacing both invertebrate and vertebrate species. Restoration of west coast dunes through the removal of Ammophila began in the 1990s. Methods usually consist of one or a combination of manual digging, burning/herbicides, or excavation with heavy equipment. There are benefits and disadvantages to each method. Manual removal has proven most effective at restoring foredune form and process but is expensive. Excavation and herbicides may result in the loss of foredune morphology. Managers must articulate goals carefully before selecting restoration methods.