Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches

Responses of methane production and methanogenic pathways to polystyrene nanoplastics exposure in paddy soil

Nanoplastics (NPs) have attracted increasing attention within terrestrial ecosystems. However, our understanding of their impacts on the intricate anaerobic methanogenesis processes occurring in paddy soils microbial communities remains limited with respect to nanoplastics shape, function, and metabolic effects. Herein, we explored the effects of polystyrene nanoplastics (PS-NPs) and microplastics (PS-MPs) on anaerobic methanogenesis in a typical paddy soil. The results show that PS-NPs delayed methane production and the time to reach peak acetate content in incubation process of paddy soils, and the methanogenic rate increased rapidly after 13 days, with a maximum increase of 87.97%. However, PS-MPs had no marked effect on CH4, CO2 and acetate production. In addition, PS-NPs affected soil physicochemical properties by reducing pH and increasing electrical conductivity. Acetoclastic methanogens were enriched and the relative abundance of the genes ackA, pta, ACSS, cdhC, cdhD and cdhE in the acetoclastic pathways were significantly increased under PS-NPs exposure. In addition, PS-MPs had significant effect on the microbial community structure but no effect on methanogenic pathways of the paddy soils. This study provides important insights into the response of key microorganisms, functional genes and methanogenesis pathways to NPs during anaerobic methanogenesis in paddy soils.

In silico analysis of comparative affinity of phytosiderophore and bacillibactin for iron uptake by YSL15 and YSL18 receptors of Oryza sativa

Iron is an important micronutrient for plant growth and development. In the case of Oryza sativa, iron is made available primarily with the help of iron chelators called phytosiderophores i.e. variants of deoxymugineic acid (DMA). They bind with ferric ions and get internalized through Yellow Stripe Like transporters viz. YSL15 and YSL18. However, due to low amount of secretion of phytosiderophores, rice suffers from iron deficiency. Alternatively, siderophores of plant growth promoting rhizobacteria may support iron uptake and make it available to plants via transporting ferric ions possibly through the same transporters. Present study aims to assess comparative binding of DMA and a xenosiderophore (siderophores used by organisms other than the ones producing them) of rhizobacteria i.e. bacillibactin with Fe³⁺ ion and subsequent transporters of rice. Protein-protein interaction and gene expression analysis predicts uptake of Fe³⁺ by YSL15 from the rhizosphere region and further distribution through YSL18 with the help of various predicted functional partners. Docking studies confirm the thermodynamically more favourable structure of bacillibactin-Fe³⁺ complex than DMA-Fe³⁺ complex. Molecular modelling of YSL15 and YSL18 was done through ab initio method and their evaluation by Ramachandran plot, ProSA, ERRAT value and verify 3 D score revealed a good quality models. Comparative binding assessment through docking and molecular dynamics simulation suggests better binding energies of YSL transporters with bacillibactin-Fe³⁺ complex as compared to DMA-Fe³⁺ complex. The current study suggests possible application of xenosiderophores of PGPR origin in supporting plant growth via iron uptake and distribution in rice.Communicated by Ramaswamy H. Sarma.

Management for Paddy, Oil Palm, and Pineapple Plantations in Malaysia: Current Status and Reviews

Heavy rainfall causes a loss of fertiliser to the environment, and it leads to environmental issues such as eutrophication. Replenishment of fertiliser to replace the loss imposes a financial impact since frequent applications are costly and labour intensive. Therefore, investigations on proper fertiliser application in maintaining good soil pH, improving plant growth, and increasing crop yield from various plantations across Malaysia are of paramount importance. Meanwhile, limited agricultural-related studies about crop management in Malaysia have been done. This study presents a state-of-the-art review of Malaysia’s paddy, oil palm, pineapple plantations, and the existing nutrient management and fertilisation practices throughout the crop cycle. A systematic study of the existing crop management in terms of farming practices, nutrient management, and fertiliser application on the plantations of paddy, oil palm, and pineapple in Malaysia was carried out. Industry overviews for these three crop types based on past situations and future directions are also included. Recommendations on how to better manage these plantations are also outlined to promote a better understanding of the past, current, and future direction of the agricultural activities and management for principal edible crops like paddy, oil palm, and pineapple in Malaysia.

The effect of wheat seedling density on photosynthesis may be associated with the phyllosphere microorganisms

Wheat seedlings are significantly impacted by the presence of bacteria. However, bacteria are unavoidably growing together with wheat. The study aimed to reveal wheat photosynthesis, phyllosphere bacterial community composition, and a shift in the bacterial community following different density treatments in a closed artificial ecosystem. Here, we report the relationship between photosynthesis and bacterial community in wheat seedlings for different planting densities. In this closed artificial ecosystem, a total of 30 phyla were detected, with 17 of them were simultaneously present in four treatments, under high light intensity and carbon dioxide growth environment. The key phyla detected include Firmicutes, Proteobacteria, and Bacteroidetes. We found that planting densities significantly impacted the photosynthetic characteristics of wheat and bacterial genetic biodiversity, but not on species composition of the bacterial community. Network analysis shows that the phyllosphere bacteria network structures were characterized by the clustering coefficient and modularity. Network for the 1000 plants/m² treatment group exhibits the highest levels of average clustering coefficient but lowest modularity and number of modules, among all plant densities tested. In addition, the network for the 1200 plants/m² treatment group exhibits the best characteristics in terms of net photosynthesis rate and intrinsic water use efficiency, higher complex phyllosphere community network structures, higher abundance of Corynebacterium, and more function of "Amino acid metabolism", which encourages the plants to grow better. The findings presented in this work elucidated the role of plant density in the growth of phyllosphere bacteria during wheat seedlings and provided theoretical support for reasonable wheat density cultivation in closed artificial ecosystems and wheat field production.

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.