Species detection using environmental DNA (eDNA) is a biomonitoring tool that can be widely applied to mangrove restoration and management. Compared to traditional surveys that are taxa-specific and time-consuming, eDNA metabarcoding offers a rapid, non-invasive and cost-efficient method for monitoring mangrove biodiversity and characterising the spatio-temporal distribution of multiple taxa simultaneously. General guidelines for eDNA metabarcoding are well-established for aquatic systems, but habitat-specific guidelines are still lacking. Mangrove habitats, as priority ecosystems for restoration in Southeast Asia, present unique prospects and challenges in these regards. Environmental DNA metabarcoding can be used to (1) track functional recovery in ecological restoration, (2) prioritise conservation areas, (3) provide early warning for threats, (4) monitor threatened taxa, (5) monitor response to climate change, and (6) support community-based restoration. However, these potential applications have yet been realized in Southeast Asia due to (1) technical challenges, (2) lack of standardised methods, (3) spatio-temporal difficulties in defining community, (4) data limitations, and (5) lack of funding, infrastructure and technical capacity. Successful implementation of eDNA metabarcoding in mangrove restoration activities would encourage the development of data-driven coastal management and equitable conservation programs. Eventually, this would promote Southeast Asia’s shared regional interests in food security, coastal defence and biodiversity conservation.

Bacillus pumilus strain TUAT1 is a plant growth-promoting bacterium (PGPB) applied as a biofertilizer, containing its spores, for rice. In this study, we analyzed the short-term effects of biofertilization on plant growth in the nursery and long-term effects on plant vegetative growth, yield, and lodging resistance in paddy fields using animal feed rice (‘Fukuhibiki’ and line LTAT-29 which was recently officially registered as a cultivar ‘Monster Nokodai 1′) and fodder rice (line TAT-26). The effects of the biofertilization were analyzed under two nitrogen treatments and at two transplanting distances in the field. The application of 10⁷ colony forming units (CFU) mL⁻¹ bacterial spore solution to seeds on plant box significantly improved the initial growth of rice. The biofertilizer treatment with this strain at 10⁷ CFU g⁻¹ onto seeds in nursery boxes increased the nitrogen uptake at the early growth of rice in the field, resulting in higher growth at the late vegetative growth stage (e.g., tiller number and plant height). Furthermore, the improvement of growth led to increases of not only yield components such as the total panicle number (TPN) and the number of spikelets in a panicle (NSP) in LTAT-29 but also the straw yield and quality of TAT-26. The lodging resistances of these forage rice plants were also improved due to the increased root development and photosynthesis creating tougher culms.

Aluminum (Al) toxicity is a major problem affecting soil fertility, microbial diversity, and nutrient uptake of plants. Rhizobia response and legume interaction under Al conditions are still unknown; it is important to understand how to develop and improve legume cultivation under Al stress. In this study, rhizobia response was recorded under different Al concentrations. Al effect on rhizobial cells was characterized by combination with different two pH conditions. Symbiosis process was compared between α- and β-rhizobia inoculated onto soybean varieties. Rhizobial cell numbers was decreased as Al concentration increased. However, induced Al tolerance considerably depended on rhizobia types and their origins. Accordingly, organic acid results were in correlation with growth rate and cell density which suggested that citric acid might be a positive selective force for Al tolerance and plant interaction on rhizobia. Al toxicity delayed and interrupted the plant–rhizobia interaction and the effect was more pronounced under acidic conditions. Burkholderia fungorum VTr35 significantly improved plant growth under acid–Al stress in combination with all soybean varieties. Moreover, plant genotype was an important factor to establish an effective nodulation and nitrogen fixation under Al stress. Additionally, tolerant rhizobia could be applied as an inoculant on stressful agroecosystems. Furthermore, metabolic pathways have still been unknown under Al stress.

Biofertilizers are agricultural materials capable of reducing the usage amounts of chemical fertilizers. Spore-forming microorganisms (SFM) could be used for plant growth promotion or to improve plant health. Until now, biofertilizers based on SFM have been applied for rice and other crops. In this study, we isolated and characterized SFM, which were colonized on the Oryza sativa L. roots. SFM were analyzed regarding the short-term effects of biofertilization on the nursery growths. Analysis was performed without nitrogen or any inorganic fertilizer and was divided into two groups, including bacteria and fungi. SF-bacteria were dominated by the Firmicutes group, including species from Viridibacillus, Lysinibacillus, Solibacillus, Paenibacillus, Priestia, and mainly Bacillus (50%). The fungi group was classified as Mucoromycota, Basidiomycota, and mainly Ascomycota (80%), with a predominance of Penicillium and Trichoderma species. In plant performance in comparison with B. pumilus TUAT1, some bacteria and fungus isolates significantly improved the early growth of rice, based on 48 h inoculum with 10⁷ CFU mL⁻¹. Furthermore, several SFM showed positive physiological responses under abiotic stress or with limited nutrients such as phosphorous (P). Moreover, the metabolic fingerprint was obtained. The biofertilizer based on SFM could significantly reduce the application of the inorganic fertilizer and improve the lodging resistances of rice, interactively enhancing better plant health and crop production.

Many abiotic factors have affected symbiosis effectiveness. However, the responses and interactions vary depending on the plant host, environmental factors, and symbiotic strains. The effect of various environmental factors on the competitiveness of rhizobial strains in host legumes has been examined, but many questions are still unresolved. For example, in the Rhizobia-legume symbiosis, the nitrogen fixation and nodulation processes are strongly related to the physiological state of the host plant. Therefore, a competitive and persistent rhizobial strain is not expected to express its total capacity for nitrogen fixation under limiting factors (e.g., salinity, unfavorable soil pH, nutrient deficiency, mineral toxicity, extreme temperatures, soil moisture problems, and inadequate photoperiods). Moreover, populations of rhizobial species vary in their tolerance to major environmental factors. Furthermore, this chapter emphasizes the studies on symbiosis under abiotic stress and its challenges. Additionally, this can help to understand and establish an effective biological process for improvement in agricultural productivity.