Hot Topic

Digging deep for biodiversity

Thursday, 18 January 2018  | 

The importance of soil microbes in community and ecosystem processes is widely acknowledged and yet there are few attempts to incorporate microbes into conservation and restoration practice. The oversight hampers efforts to conserve and restore native ecosystems in the face of increased environmental degradation and environmental change.

Native and non-native soil microbes interact with native and non-native plants and these interactions have implications for conservation and restoration. Invasive plants often impede conservation and restoration efforts particularly where soil mutualists co-invade. For example, the invasion of pines across the southern hemisphere has been facilitated by the spread of its ectomycorrhizal fungus, and therefore control of invasive pines may be achieved by controlling its fungus. Similarly, the recent outbreak of myrtle rust in eastern Australia, a fungal plant pathogen of global significance, is a timely reminder of the significant role of research to manage the consequences of invasion by plant pathogens in soil.

Emerging tools offer a whole of microbial community perspective. For example, new tools identified that the native critically-endangered Wollemi pine associates with species-specific fungal communities whose presence is correlated with translocation success. There are efforts too, to understand how plant-soil-microbe interactions might be influenced by other drivers of relevance to conservation and restoration. For example, recent research in temperate grasslands in southern Australia suggests fire can affect soil fungal community composition, possibly through disruption of plant-fungal associations.

New technologies, such as next generation sequencing and genome editing tools to alter gene function, allow exploration and utilisation of soil microbial communities like never before. Coupled with field-based experiments these tools offer a deeper understanding of the contribution of soil microbes to function and biodiversity outcomes of restoration and conservation.

Supporting Research

Janos, D. P., Scott, J., Aristizábal, C., & Bowman, D. M. (2013). Arbuscular-mycorrhizal networks inhibit Eucalyptus tetrodonta seedlings in rain forest soil microcosms. Plos One, 8, e57716.
To assess whether rain forest arbuscular mycorrhizal (AM) networks inhibit Eucalyptus tetrodonta seedlings. Additionally, to test whether iron deficiency limited E. tetrodonta growth.
Standish, R. J., Stokes, B. A., Tibbett, M., & Hobbs, R. J. (2007). Seedling response to phosphate addition and inoculation with arbuscular mycorrhizas and the implications for old-field restoration in Western Australia. Envir. Exper. Bot. 61, 58-65.
To test that P-fertiliser residues will limit the establishment of native plant species and their mycorrhizas to old-fields in the wheat-growing region (i.e. the wheatbelt) of Western Australia.
Rigg, J. L., Offord, C. A., Zimmer, H., Anderson, I. C., Singh, B. K., & Powell, J. R. (2017). Conservation by translocation: establishment of Wollemi pine and associated microbial communities in novel environments. Plant Soil, 411, 209-225.
The goal was to identify relationships associated with biotic and abiotic characteristics and outcomes of a Wollemi pine translocation event, and to use this information to advise future targeted translocation to ensure effective conservation of the critically endangered Wollemi pine
Birnbaum, C., Bissett, A., Thrall, P. H., & Leishman, M. R. (2014). Invasive legumes encounter similar soil fungal communities in their non-native and native ranges in Australia. Soil Biol.Biochem.76, 210-217.
To assess intra- and interspecific variation in the soil fungal communities of five invasive legumes native to either south-east or south-west Australia
Hamonts, K., Bissett, A., Macdonald, B. C., Barton, P. S., Manning, A. D., & Young, A. (2017). Effects of ecological restoration on soil microbial diversity in a temperate grassy woodland. Appl. Soil Ecol. 117, 117-128.
To quantify the response of soil bacterial and fungal communities to restoration treatments, variation in microhabitat elements and vegetation in a critically endangered Australian box-gum grassy woodland ecosystem.
Prober, S. M., Bissett, A., Walker, C., Wiehl, G., McIntyre, S., & Tibbett, M. (2015). Spatial structuring of arbuscular mycorrhizal communities in benchmark and modified temperate eucalypt woodlands. Mycorrhiza, 25, 41-54.
1.What AMF occur within benchmark woodlands (no agricultural management history) and what are their patterns of spatial structuring at regional, patch and fine scales?2.What changes in AMF composition and heterogeneity occur in woodlands that are modified or replaced by agricultural practices at site scales?3.Do current revegetation activities restore AMF composition?
Dickie, I. A., Nuñez, M. A., Pringle, A., Lebel, T., Tourtellot, S. G., & Johnston, P. R. (2016). Towards management of invasive ectomycorrhizal fungi. Biol. Inv. 18, 3383-3395.
1. Provide a brief overview of the history and effects of ectomycorrhizal fungal invasions, 2. Discuss prevention, detection, and removal strategies for new incursions, recognizing proposed strategies are based on expert opinion and analogy to plant and animal invasions, and 3. Consider strategies to manage invasions and reduce the rate of spread, where removal is impossible.
Wubs, E. J., van der Putten, W. H., Bosch, M., & Bezemer, T. M. (2016). Soil inoculation steers restoration of terrestrial ecosystems. Nature plants, 2, 16107.
To test the possibility of community steering through application of soil inocula in the field byanalysing a large-scale, well-replicated, soil inoculation experiment on soils that had been used forarable farming for several decades.
Calderón, Kadiya, et al. (2017) Effectiveness of ecological rescue for altered soil microbial communities and functions. The ISME journal 11.1: 272-283.
Examined the effectiveness of introducing microbial communities in altered communities, to recover soil biodiversity and functioning.Hypothesized that priority effects and the biodiversity level of the already-established communities but also of the newly introduced communities are of importance for community assembly and successful restoration.
Romero-Olivares, A. L., Allison, S. D., & Treseder, K. K. (2017). Soil microbes and their response to experimental warming over time: A meta-analysis of field studies. Soil Biol. Biochem. 107, 32-40.
A meta-analysis on 25 field experiments to examine how warming effects on soil respiration, microbial biomass, and soil microbial C respond to the duration of warming.
Koziol, L., & Bever, J. D. (2016). The missing link in grassland restoration: arbuscular mycorrhizal fungi inoculation increases plant diversity and accelerates succession. J. Appl. Ecol.54, 1301-1309
(i) Do early or late successional plants respond differently to AM fungal species? (ii) Is plant community richness, diversity or seed recruitment influenced amendment with AM fungal species? (iii) Does a diverse mixture of AM fungal species affect plant response differently than inoculation with single species of AM fungi? 
Fajardo, L., Cáceres, A., & Arrindell, P. (2014). Arbuscular mycorrhizae, a tool to enhance the recovery and re-introduction of Juglans venezuelensis Manning, an endemic tree on the brink of extinction. Symbiosis, 64, 63-71.
To evaluate the effects of two arbuscular mycorrhizal fungi (AMF), Dentiscutata heterogama and Rhizophagus manihotis on the growth and nutrition of Juglans venezuelensis Manning.
Egidi, Eleonora, et al. (2016) Fire regime, not time-since-fire, affects soil fungal community diversity and composition in temperate grasslands. Fems microb. Lett. 363.17.
To assess the effect of fire frequency and time-since-last-fire in Themede triandra-dominated graslands on soil fungal communities.
Burgess, Treena I., et al. (2016) Tree invasions and biosecurity: eco-evolutionary dynamics of hitchhiking fungi. AoB Plants 8.
Assess and describe fungal functional groups with ten different life history strategies, providing examples for these tree associated fungi (including oomycetes), their transport and introduction, and, using the EEE (Eco-evolutionary) platform, predict the potential of the different groups to establish and spread into the natural environment.
Doudna, Jennifer A., and Emmanuelle Charpentier. (2014). The new frontier of genome engineering with CRISPR-Cas9. Science 346.6213: 1258096.
Review the CRISPR biology from initial discovery to CRISPR-Cas9 enzyme mechanism which is a new technology to modify, regulate, or mark genomic loci in organisms from all three domains of life.
unez MA, Dickie IA 2014 Invasive belowground mutualists of woody plants. Biological Invasions 16: 645-661
Discuss plant invasion from perspective of soil biota
Tobais PA, Guest DI, Kulheim C, Hsieh JF, Park RF 2016 A curious case of resistance to a new encounter pathogen: myrtle rust in Australia. Molecular Plant Pathology 17: 783-788.
To examine resistance of myrtaceous plant species to invasive pathogen (the rust)
Carnegie AJ, Kathuria A, Pegg GS, Entwistle P, Nagel M, Giblin FR 2016 Impact of the invasive rust Puccinia psidii (myrtle rust) on native Myrtaceae in natural ecosystems in Australia. Biological Invasions 18: 127-144.
To understand potential threat of rust to native ecosystems in eastern Australia using two rainforest plant species as indicators.
Delgado‐Baquerizo, M., Powell, J. R., Hamonts, K., Reith, F., Mele, P., Brown, M. V., ... & Singh, B. K. (2017). Circular linkages between soil biodiversity, fertility and plant productivity are limited to topsoil at the continental scale. New Phyt, 215, 1186-1196.
To investigate the continental-scale relationships between the diversity of microbial and invertebrate-based soil food webs, fertility and above-ground plant productivity at 289 sites and two soil depths, that is 0–10 and 20–30 cm, across Australia.