Conversion of a High-Altitude Temperate Forest for Agriculture Reduced Alpha and Beta Diversity of the Soil Fungal Communities as Revealed by a Metabarcoding Analysis

Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment

Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.

Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects

Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.

Biochars modify the degradation pathways of dewatered sludge by regulating active microorganisms during gut digestion of earthworms

Biochar can accelerate the degradation and mineralization of organic matter during vermicomposting of sludge and the resulted vermicompost is termed as vermi-char containing active enzymes and microorganisms. However, the mechanisms by which biochars affect vermicomposting of the dewatered sludge during gut digestion of earthworms remain unclear. This study aimed to investigate the effects of biochar on the degradation pathways of organic matter and the involved active microorganisms in dewatered sludge during gut digestion of earthworms. The earthworms Eisenia fetida were fed on three sludge substrates; 1) sludge mixed with 5% corncob biochar, 2) sludge mixed 5% rice husk biochar, and 3) sludge without biochar. The results showed that dissolved organic carbon significantly decreased by 5.65%-21.81% after the 5-day gut digestion of earthworms (P < 0.05) and that biochar addition could accelerate the decomposition of aromatic protein-like substances. Contrarily, the nitrate in earthworms casting with biochars significantly increased by 47.32%-122.64% (P < 0.05) compared with the control. The numbers of active bacteria and eukaryotes in earthworm castings with biochars significantly enhanced by 1.34-1.45 times and 0.45-5.91 times, respectively, than the control (P < 0.05). Active Actinobacteria and Bacteroidetes dominated the castings with biochars significantly enriched by 76.18%-88.83% and 4.02%-18.59% (P < 0.05), respectively, compared to control. As for eukaryotes, the biochars amendment increased Cercozoa abundance by 114.23%-136.31% but decreased Annelida by 55.61%-75.88% in the castings. The partial least squares path model revealed that the biochars could change the content and structure of organic matter in earthworm castings during vermicomposting of sludge by affecting environmental factors, microbial abundance, and microbial community composition.