Article
Microbiology
Lu Yang, Jun Chen
Summary: This study provides a comprehensive evaluation of existing differential abundance analysis (DAA) tools, revealing that none of the evaluated methods are simultaneously robust, powerful, and flexible. To overcome the challenge of selecting the best DAA tool, the researchers designed an optimized procedure called ZicoSeq, which combines the strengths of existing methods and can be applied to diverse microbiome datasets for robust biomarker discovery.
Article
Environmental Sciences
Jiaoyang Zhang, Zemin Ai, Hongwei Xu, Hongfei Liu, Guoliang Wang, Lei Deng, Guobin Liu, Sha Xue
Summary: Plant-soil feedback (PSF) is an important driver of plant community dynamics, with early successional plant species having a positive feedback effect on soil and subsequent plant species showing a negative feedback effect. The microbial responses to PSF vary with different plant successional stages, influencing the plant community composition.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemical Research Methods
Molly G. Hayes, Morgan G. I. Langille, Hong Gu
Summary: This study proposes an ensemble approach for cross-study exploratory analyses of microbial abundance data by estimating the variance-covariance matrix of underlying abundances from each dataset and modeling these covariances jointly to find a shared low-dimensional subspace. By projecting the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, likely to reflect more generalizable biological signal. The approaches show good performance on simulated and real metagenomic data in terms of signal retention and interpretability, with a recommended implementation.
BMC BIOINFORMATICS
(2023)
Review
Agriculture, Multidisciplinary
Zhen Wang, Xiaohu Hu, Manoj Kumar Solanki, Fei Pang
Summary: Microbes play a crucial role in the rhizosphere ecology and have a significant impact on plant health. The advancement of gene sequencing technology has greatly contributed to the understanding of plant microbiome structure and function. This Review explores the biological control pathways of plant-associated microbiomes and their functions in enhancing plant defense against pathogens. It also emphasizes the need to develop smart agriculture practices using synthetic microbial communities (SynComs) for plant disease control and the exploration of new microbial resources.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Review
Biotechnology & Applied Microbiology
Leandro Pereira-Dias, Paulo R. Oliveira-Pinto, Juliana O. Fernandes, Laura Regalado, Rafael Mendes, Catia Teixeira, Nuno Mariz-Ponte, Paula Gomes, Conceicao Santos
Summary: Agricultural systems require low-cost, safe antibiotics to protect crops from pests and diseases. Peptaibiotics have shown potential as alternatives to agrochemicals, with antibacterial, antifungal, and antiviral activity, and the ability to induce plant resistance against phytopathogens. However, their low solubility and difficulty in synthesis and purification have limited their application in agriculture. This review provides a comprehensive analysis of peptaibiotics, including their classification, biosynthesis, relevance to plant protection, and mode of action against phytopathogens, as well as strategies to enhance their solubility and production.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Plant Sciences
Prachi Singh, Jyoti Singh, Shatrupa Ray, Anukool Vaishnav, Priyanka Jha, Rakesh Kumar Singh, Harikesh Bahadur Singh
Summary: Microbial volatile organic compounds (mVOCs) and their potential in plant growth and development remains understudied. In vitro experiments demonstrated that volatiles from Trichoderma asperellum BHU P1 and Ochrobactrum sp. BHU-PB1 inhibited the growth of Fusarium oxysporum f.sp lycopersici (FOL). Exposure to volatiles from Ochrobactrum sp. resulted in the highest seed germination and seedling growth. Compared to the control, plants treated with microbial volatile metabolites exhibited better growth parameters and lower disease incidence.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Imane Chamkhi, Taoufiq Benali, Tarik Aanniz, Naoual El Menyiy, Fatima-Ezzahrae Guaouguaou, Nasreddine El Omari, Mohamed El-Shazly, Gokhan Zengin, Abdelhakim Bouyahya
Summary: Plants and microbes interact through various chemical signaling pathways, with microbes secreting elicitors that trigger biological responses in plants via specific receptors. These elicitor molecules induce changes in phenotype and stimulate the synthesis of secondary metabolites in plants. Different microorganisms release elicitors that activate signaling pathways involved in the synthesis of bioactive compounds in plants, which can be explored for drug discovery purposes.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Review
Plant Sciences
Hisashi Kato-Noguchi, Midori Kato
Summary: Chromolaena odorata is an invasive species that has naturalized in several countries in tropical Asia, Austria, and West Africa. It negatively impacts native species diversity and populations, and is considered a noxious weed in agricultural fields. The species possesses defense mechanisms against natural enemies and allelopathic potential, which contribute to its invasiveness.
Review
Plant Sciences
Lorena I. Rangel, Melvin D. Bolton
Summary: Plants have various responses to counter disease, while plant pathogens orchestrate a finely tuned repertoire of virulence mechanisms. Secondary metabolite effectors (SMEs) play important roles in plant disease, including self-resistance and manipulation of the microbial community.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Review
Microbiology
Johannes Mapuranga, Jiaying Chang, Lirong Zhang, Na Zhang, Wenxiang Yang
Summary: Fungal plant pathogens employ proteinaceous and non-proteinaceous effectors, including secondary metabolites (SMs) and small non-coding RNAs (sRNAs), to manipulate the host plant's defense system. While much research has focused on secreted effector proteins, the roles of fungal SMs and sRNAs have been largely overlooked. Fungal SMs are generated during plant colonization, especially in early infection stages, while fungal sRNAs target plant genes involved in resistance and defense responses. Understanding the functions of these effectors can provide insights into the infection process and host genes targeted. This review discusses the roles of fungal SMs and sRNAs in plant-fungal interactions, translocation of sRNA effectors across kingdoms, and the application of cross-kingdom RNA interference in managing plant diseases.
Article
Microbiology
Xinxin Liu, Xiaoxiao Li, Yinfeng Hua, Aki Sinkkonen, Martin Romantschuk, Yanfang Lv, Qian Wu, Nan Hui
Summary: This study found that meat and bone meal (MBM) can be an effective additive in composting, as it stabilizes pH and extends the thermophilic phase. Compared to urea, MBM treatment resulted in a 24.76% increase in germination index, higher microbial diversity, and different community compositions. Organic matter and pH were identified as the most significant factors influencing bacterial and fungal community structure. MBM addition also reduced the abundance of pathogenic fungi.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Yueling Qi, Adam Ossowicki, Etienne Yergeau, Gianpiero Vigani, Violette Geissen, Paolina Garbeva
Summary: Plastic mulch film residues did not significantly impact soil suppressiveness level in the short term, but created a new niche plastisphere housing a unique microbial community dominated by potential fungal pathogens.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Article
Environmental Sciences
Tao Jiang, Matt Geisler, Weilan Zhang, Yanna Liang
Summary: This study found that ether-PFAS significantly affected the structure and functions of soil microbial communities, especially showing differences at different concentrations.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Microbiology
Andree S. George, Maria T. Brandl
Summary: Plant innate immunity shows potential as a host-based defense strategy against enteric pathogens, releasing antimicrobial phytochemicals in response to threats; these phytochemicals may create intrinsic barriers to the survival and multiplication of enteric pathogens in plants through their antagonistic activity.
Review
Plant Sciences
Maryam Shahrtash, Shawn P. Brown
Summary: This review discusses the potential of incorporating plant-microbe and microbe-microbe interactions into invasive plant management strategies. The authors advocate for increased research in this area to diversify sustainable control options.