Soil bacterial communities and their associated functions for forest restoration on a limestone mine in northern Thailand

Abstract

Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommended, to accelerate soil ecosystem restoration and support vegetation recovery. Moreover, if inoculation is included in mine rehabilitation programs, the genera: Bacillus, Streptomyces and Arthrobacter are likely to be of particular interest, since these genera can be cultivated easily and this study showed that they can survive under the extreme conditions that prevail on opencast mines.

Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

“…humic acid or salt) that can limit the recovery of microbes during DNA extraction and amplification [41,42]. Moreover, bias of PCR primers and low abundance of DNA could also be an issue [12,43]. However, eDNA-based amplicon sequencing can still be a valuable approach for exploring information on microbial diversity, community composition and their response to natural or human-induced changes e.g., [44][45][46].…”

“…Another promising application of this method would be possible on soil samples that contain extremely low microbial abundance or high inhibitors. Sansupa et al [43] showed that this method can be used to identify viable bacteria that survived in extreme soil conditions in mining areas where microbial DNA cannot be efficiently extracted. Based on these results, some potential soil bacteria are suggested for use as materials for restoration/rehabilitation of highly degraded soil in a limestone mine area.…”

Identification of Microorganisms Dwelling on the 19th Century Lanna Mural Paintings from Northern Thailand Using Culture-Dependent and -Independent Approaches

“…Microbial communities in environmental samples can be assessed based on various culture-dependent and culture independent approaches or a combination of both approaches [ 25 , 26 , 27 ] The culture-dependent approach is a primary method employed to investigate the culturable viable microorganism in the environmental sample [ 27 , 28 ]. This conventional method is based on isolation techniques using various media culture types and, depending on microbial physiological requirements, different taxa and communities can be isolated [ 27 , 29 ].…”

Rewilding and restoring nature in a changing world

“…The two main themes that emerge from the collection are related to restoration success stories (>40%) and best practices in restoration around the globe (>30%). The selected studies in this Collection, which cover six continents and at least 13 countries, were carried out in diverse settings and contexts, such as marine, fresh water and terrestrial habitats including forests and grasslands, rivers and coastal areas, woodlands, wetlands, and mountains (e.g., Sansupa et al [3], Broughton et al [4], Schulz et al [5], Ndangalasi et al [6]). Features of interest included in this Collection span from bacteria through large vertebrates (e.g., wild dogs, elephants) to ecosystems and their functions.…”

“…As shown in this Collection and in other studies, trade-offs in restoration efforts are not uncommon and ultimately, restoration is successful when we can achieve restoration goals while minimizing trade-offs. The successful stories from the restoration interventions across different habitats and species showcased in the Collection (e.g., Sansupa et al [3], Roon et al [18], Valach et al [21], Bouley et al [23]) are a valuable addition to the science needed to advocate for restoration as a pathway to the recovery of previously degraded, damaged, or destroyed ecosystems. Reporting successful restoration outcomes can help increase buy-in for further restoration projects and increase funding availability for such projects.…”