Article
Biochemistry & Molecular Biology
Jason R. Grant, Eric Enns, Eric Marinier, Arnab Mandal, Emily K. Herman, Chih-yu Chen, Morag Graham, Gary Van Domselaar, Paul Stothard
Summary: Proksee is a powerful and user-friendly system for assembling, annotating, analyzing, and visualizing bacterial genomes. It accepts various file formats and provides unique assembly metrics, a high-performance genome browser, embedded analysis tools, and the option to export data for sharing and reproducibility. The system is designed to scale and ensure a robust and responsive web server.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Food Science & Technology
Anton E. Shikov, Iuliia A. Savina, Anton A. Nizhnikov, Kirill S. Antonets
Summary: Bacterial organisms have undergone homologous recombination and horizontal gene transfer multiple times, resulting in enhanced adaptation to new environments, specialization, the emergence of new species, and changes in virulence. Analysis of genomic studies of bacterial species in the past 30 years reveals that these genetic exchanges are associated with ecological diversification, pathogenesis, and symbiosis.
Article
Biotechnology & Applied Microbiology
Robin Jugas, Karel Sedlar, Martin Vitek, Marketa Nykrynova, Vojtech Barton, Matej Bezdicek, Martina Lengerova, Helena Skutkova
Summary: CNV detection in bacteria is less focused on compared to eukaryotes, but with increasing interest due to challenges in bacterial drug resistance. CNproScan is a bacterial genome CNV detection method that can detect shorter events and provide classification, showing improvements over existing methods.
Article
Microbiology
Laura Carrilero, Anastasia Kottara, David Guymer, Ellie Harrison, James P. J. Hall, Michael A. Brockhurst
Summary: Plasmids play a crucial role in bacterial evolution by transferring functional genes between lineages, driving genomic diversification. Plasmid coexistence in bacterial genomes is stably maintained through compensatory evolution to reduce fitness costs, unless positive selection for plasmid-borne gene functions is present. Positive selection leads to unstable plasmid coexistence, discriminating between differential fitness benefits of functionally redundant plasmid replicons. This study helps explain the forces structuring bacterial genomes, highlighting the importance of rare positive selection or nonredundancy of accessory gene functions among coexisting plasmids.
Article
Biochemistry & Molecular Biology
Fatemeh Sharifi, Yuzhen Ye
Summary: Reverse transcriptases (RTs) play various roles in different systems in prokaryotes, but there is a lack of computational tools for their identification and characterization. Researchers developed a tool called myRT to identify and classify prokaryotic RTs, providing genomic neighborhood information.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Oncology
Axel Rosendahl Huber, Cayetano Pleguezuelos-Manzano, Jens Puschhof
Summary: Changes in the microbiome are linked to colorectal cancer development, with certain bacteria inducing mutational patterns present in colorectal cancer genomes. More research is needed to understand the microbial role in oncogenic mutation induction, cancer development, and preventive strategies.
BRITISH JOURNAL OF CANCER
(2021)
Article
Biochemistry & Molecular Biology
Alix Corneloup, Anne Caumont-Sarcos, Alain Kamgoue, Brigitte Marty, Phan Thai Nguyen Le, Patricia Siguier, Catherine Guynet, Bao Ton-Hoang
Summary: REP, diverse palindromic DNA sequences found at high copy number in many bacterial genomes, have important roles in cell physiology. In vitro experiments reveal the interaction between TnpA(REP) and REPs with different structures.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Martin Klapper, Alexander Huebner, Anan Ibrahim, Ina Wasmuth, Maxime Borry, Veit G. Haensch, Shuaibing Zhang, Walid K. Al-Jammal, Harikumar Suma, James A. Fellows Yates, Jasmin Frangenberg, Irina M. Velsko, Somak Chowdhury, Rosa Herbst, Evgeni Bratovanov, Hans-Martin Dahse, Therese Horch, Christian Hertweck, Manuel Ramon Gonzalez Morales, Lawrence Guy Straus, Ivan Vilotijevic, Christina Warinner, Pierre Stallforth
Summary: Major advances in ancient DNA research have allowed access to paleogenomic diversity, however, the functions and capabilities of this genetic material remain largely unknown. In this study, dental calculus samples from ancient humans were examined, leading to the discovery of a biosynthetic gene cluster that produces previously unknown metabolites called paleofurans. This demonstrates the possibility of obtaining natural products from ancient organisms and opens up new opportunities for exploration in this field.
Review
Biochemical Research Methods
Zhaoqian Liu, Jingtong Feng, Bin Yu, Qin Ma, Bingqiang Liu
Summary: Bacterial genomes are recognized to closely interact with cellular processes. Researchers focus on uncovering organizational mechanisms of bacterial genomes to reveal potential cellular activities. Advances in experimental techniques and computational models provide opportunities for understanding these mechanisms, including local structures such as operons/transcription units and global constraints shaping bacterial genomes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Mostafa M. H. Ellabaan, Christian Munck, Andreas Porse, Lejla Imamovic, Morten O. A. Sommer
Summary: Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes. Researchers identified potential mobilization elements and other features associated with ARG transfer among bacterial clades, predicting the potential future dissemination of known ARGs.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Pengfei Zhang, Dike Jiang, Yin Wang, Xueping Yao, Yan Luo, Zexiao Yang
Summary: This study compared different assembly strategies for Haemophilus parasuis, a bacterium causing Glasser's disease in swine, and found that assembly with PacBio or ONT reads followed by polishing with Illumina reads resulted in high-quality genome reconstruction. Additionally, correction with Homopolish after ONT-only assembly was equally effective. Aligning transcripts to assembled genomes revealed that ONT assembly errors were mainly insertions and deletions in homopolymer regions, affecting protein prediction. Polishing can fill indels and correct mistakes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Genetics & Heredity
Junjie Tan, Joachim Forner, Daniel Karcher, Ralph Bock
Summary: Genome editing has revolutionized biological research, with CRISPR/Cas-based editing being the preferred technology due to its simplicity and flexibility. Fusion of Cas nucleases with large protein domains allows for combination of DNA recognition properties with new enzymatic activities. Base editors and prime editors, produced by fusion with nucleoside deaminase or reverse transcriptase domains, induce site-specific alterations of a few nucleotides without generating double-strand breaks. Protein-only genome editing reagents based on transcription activator-like effectors have expanded base editing to chloroplast and mitochondrial genomes. This review summarizes current base editing methods for nuclear and organellar genomes, highlighting advances in precision, specificity, and efficiency, as well as discussing limitations and future challenges. In addition, applications in agricultural biotechnology and gene therapy are briefly overviewed.
TRENDS IN GENETICS
(2022)
Article
Ecology
Elizabeth G. Wilbanks, Hugo Dore, Meredith H. Ashby, Cheryl Heiner, Richard J. Roberts, Jonathan A. Eisen
Summary: The plasticity of bacterial and archaeal genomes makes it challenging to recover complete genomes from metagenomes. In this study, the researchers used strain-specific patterns of DNA methylation to successfully resolve complex bacterial genomes from metagenomic data. They recovered the largest and most complex circularized bacterial genome ever recovered from a metagenome and identified instances of horizontal gene transfer, phage infection, and strain-level structural variation.
Article
Biology
Sergio Arredondo-Alonso, Anna K. Pontinen, Francois Cleon, Rebecca A. Gladstone, Anita C. Schurch, Pal J. Johnsen, Orjan Samuelsen, Jukka Corander
Summary: The introduction of long-read sequencing technologies allows for bridging contiguous sequences into complete genomes, although the higher costs limit the number of bacterial isolates that can be long-read sequenced. The 96 barcoding kit from Oxford Nanopore Technologies successfully generated near-complete chromosomal sequences for 96 Escherichia coli isolates. The combination of ONT sequencing data with short-read sequencing data is still highly desirable to achieve optimal genome accuracy and completeness.
Article
Multidisciplinary Sciences
Ben S. Carlson, Shay Rotics, Ran Nathan, Martin Wikelski, Walter Jetz
Summary: Individual variation plays a key role in shaping environmental niche associations, with individual environmental niches of white storks showing high consistency over time and a tendency towards moderate to strong niche specialization.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Na Zhang, Chengzhi Zhu, Zongzhuan Shen, Chengyuan Tao, Yannan Ou, Rong Li, Xuhui Deng, Qirong Shen, Francisco Dini-Andreote
Summary: Beneficial host-associated bacteria can help plants defend against pathogens and specific microbial taxa can induce plant systemic resistance. The soil legacy has a significant impact on disease suppression and plant immune responses, with differences in root-associated bacterial communities and gene expression pathways associated with phenylpropanoid biosynthesis. Specific microbial taxa, including Gp6, Actinomarinicola, Niastella, Phaeodactylibacter, Longimicrobium, Bythopirellula, Brevundimonas, Ferruginivarius, Kushneria, Methylomarinovum, Pseudolabrys, Sphingobium, Sphingomonas, and Alterococcus, are correlated with genes in the phenylpropanoid biosynthesis pathway.
Article
Soil Science
Yasmin Florentino Rodrigues, Fernando Dini Andreote, Antonio Marcos Miranda Silva, Armando Cavalcante Franco Dias, Rodrigo Gouvea Taketani, Simone Raposo Cotta
Summary: We hypothesized a positive correlation between soil bacterial diversity and phosphorus availability from soluble or less soluble sources under maize cultivation. This hypothesis was evaluated using a mesocosm experiment and the dilution-to-extinction methodology to generate a gradient of soil bacterial diversity. The results showed a negative correlation between bacterial diversity index and labile P fraction in soil, as well as P content in maize. Enrichment of P-mineralizing microorganisms was observed at higher microbial dilutions, potentially affecting plant development.
APPLIED SOIL ECOLOGY
(2023)
Article
Biodiversity Conservation
Alexandre Pedrinho, Lucas William Mendes, Felipe Martins do Rego Barros, Luis Fernando Merloti, Mayara Martins E. Martins, Simone Raposo Cotta, Fernando Dini Andreote, Siu Mui Tsai
Summary: Land-use change has negative impacts on the biodiversity of plants and animals, but studies on the impacts of land-use change on soil microorganisms, particularly those involved in the phosphorus transformation processes, are lacking. This study used DNA-metagenomic sequencing and P fractionation analysis to assess the effects of forest-to-pasture conversion on soil bacterial groups involved in P transformation processes. The results showed that land-use change altered soil P dynamics and bacterial community structure.
ECOLOGICAL INDICATORS
(2023)
Article
Microbiology
Lu Luan, Guangping Shi, Guofan Zhu, Jie Zheng, Jianbo Fan, Francisco Dini-Andreote, Bo Sun, Yuji Jiang
Summary: This study investigates the geographical distribution and assembly mechanisms of different bacterial sub-communities in paddy soils across East Asia. The results show significant distance-decay relationships (DDRs) in the geographical patterns of four bacterial sub-communities. Niche breadth and dispersal rates contribute to the differences in community assembly of abundant and rare taxa, directly affecting the strength of DDRs.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Agronomy
Felipe Fadel Sartori, Thaise Dieminger Engroff, Thais H. Godoy Sanches, Julia M. Soave, Mila Victorio Pessotto, Guilherme Felisberto, Valter E. Hilgemberg Jr, Andre Froes de Borja Reis, Mariangela Hungria, Marco A. Nogueira, David de Souza Jaccoud-Filho, Fernando Dini Andreote, Durval Dourado-Neto
Summary: Biological nitrogen fixation is essential for the development of soybean plants, but management decisions such as pesticide use and timing of Bradyrhizobium sp. inoculation can negatively impact soybean growth and yield. This study evaluates the effects of pre-inoculating soybean seeds with Bradyrhizobium sp. and pesticides seed treatment on biological nitrogen fixation under laboratory, greenhouse, and field conditions. The results show that both pre-inoculation and pesticide seed treatment can reduce the recovery of Bradyrhizobium colonies, ureides concentration, biological nitrogen fixation efficiency, and plant growth. Field experiments also demonstrate that specific pesticides can cause significant yield loss and that inoculation closer to sowing can lead to higher grain weight.
EUROPEAN JOURNAL OF AGRONOMY
(2023)
Article
Microbiology
Ingrid P. Zwar, Caterina do Valle Trotta, Ana B. S. Ziotti, Milton Lima Neto, Welington L. Araujo, Itamar S. de Melo, Cristiane A. Ottoni, Ana O. de Souza
Summary: In this study, two strains of actinomycetes were isolated from Brazilian soil and mangrove sediment, and silver nanoparticles (AgNPs) were synthesized and characterized. The AgNPs exhibited antifungal activity against phytopathogens without phytotoxic effects on rice plants. Therefore, these AgNPs have the potential to be used as biocontrol agents against plant pathogens.
JOURNAL OF BASIC MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Jian-Hong Li, Mehtab Muhammad Aslam, Yang-Yang Gao, Lei Dai, Ge-Fei Hao, Zhong Wei, Mo-Xian Chen, Francisco Dini-Andreote
Summary: Microorganisms in the rhizosphere and phyllosphere of plants play important roles in plant growth and health. Recent research has shown that specific plant-associated microbes contribute to systemic plant responses that enhance plant health and performance against various stresses. However, there is still limited understanding of the mechanisms involved in microbiome-mediated signal transduction in plants. This review provides an overview of long-distance signaling mechanisms in plants mediated by plant-associated microbiomes, exploring the concept of plants and microbes as a holobiont and discussing the key molecules and mechanisms associated with plant-microbe interactions and signal transduction-induced changes in plant physiology.
TRENDS IN MICROBIOLOGY
(2023)
Article
Microbiology
Gordon F. Custer, Maya Gans, Linda T. A. van Diepen, Francisco Dini-Andreote, C. Alex Buerkle
Summary: The concept of core microbiome refers to the consistent presence of a set of microorganisms in multiple samples within a habitat. Different methods based on abundance and occupancy have been used to assign taxa to core microbiomes, but these methods have led to inconsistencies in ecological interpretation.
Article
Biochemistry & Molecular Biology
Xingang Zhou, Jingyu Zhang, Muhammad Khashi U. Rahman, Danmei Gao, Zhong Wei, Fengzhi Wu, Francisco Dini-Andreote
Summary: Terrestrial plants can influence the recruitment of rhizosphere microbiome in adjacent plants through root exudates, potentially affecting their growth and health. This study demonstrated that intercropping with potatoonion can create a disease-suppressive rhizosphere microbiome that protects tomato plants against Verticillium wilt disease. The root exudates from potatoonion promoted the colonization of Bacillus sp., which inhibited the growth of the pathogen and induced resistance in tomato plants.
Editorial Material
Biochemistry & Molecular Biology
Francisco Dini-Andreote, Gordon F. Custer
Summary: Fecal microbiota transplantation (FMT) is a procedure to treat microbiome imbalances in diseases, and ecological principles can inform FMT clinical trials and contribute to data interpretation. This effort will enhance the understanding of microbiome engraftment and assist in developing clinical protocols.
TRENDS IN MICROBIOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Lu Luan, Francisco Dini-Andreote, Bo Sun, Yuji Jiang
TRENDS IN MICROBIOLOGY
(2023)
Article
Agronomy
Cristiane Prezotto Silveira, Fernando Dini Andreote, Risely Ferraz-Almeida, Jardelcio Carvalho, John Gorsuch, Rafael Otto
Summary: Common fertilizers have low use efficiency due to nutrient losses, limiting crop production. Inoculation with Plant Growth-Promoting Bacteria (PGPB) is proposed as an alternative to increase fertilizer efficiency. This study aimed to test the hypothesis that PGPB can increase the efficiency of monoammonium phosphate (MAP), root growth, and nutrient assimilation of soybean and corn. Results showed that PGPB + MAP increased soil biological activity and crop root growth. Plant dry matter was positively correlated with soil phosphorous content, indicating increased phosphorous assimilation. In conclusion, PGPB + MAP enhances the growth and phosphorous accumulation of soybean and corn, with a direct effect on crop rooting.
Article
Soil Science
Yuji Jiang, Shuzhen Li, Andrew D. Barnes, Jia Liu, Guofan Zhu, Lu Luan, Francisco Dini-Andreote, Stefan Geisen, Bo Sun
Summary: The soil microbiome is affected by both bottom-up and top-down processes at the local soil aggregate level. Predation plays an important role in shaping the diversity and stability of soil bacterial communities, with a greater impact on macroaggregates. Predation also alters the abundance of microbial genes associated with carbon and nitrogen metabolisms.
Article
Biodiversity Conservation
Lijun Chen, Francisco Dini-Andreote, Hongqiang Liu, Huaxiang Wang, Alex Dumbrell, Zhengye Wang, Xingyu Chen, Fangfang Chen, Xiaolong Chen, Lichao Wu, Yuji Jiang
Summary: Bacteria and fungi play important roles in diverse ecosystems, and their interactions influence the structure and functioning of microbiomes. However, the impact of bacterial-fungal interactions on soil organic carbon dynamics in artificial forest ecosystems is not well understood. In this study, the soil bacterial and fungal communities were characterized in Eucalyptus plantations, and the effects of successive planting on soil carbon dynamics were investigated. The results showed that successive planting of Eucalyptus significantly altered the diversity and structure of soil bacteria and fungi, and increased the negative bacterial-fungal associations. The negative associations were associated with a decrease in soil organic carbon content and other nutrients. The study suggests that promoting short-term successive planting can mitigate the negative impact of bacterial-fungal associations on soil organic carbon decomposition.
JOURNAL OF APPLIED ECOLOGY
(2023)
Article
Food Science & Technology
Pengfa Li, Leho Tedersoo, Thomas W. Crowther, Alex J. Dumbrell, Francisco Dini-Andreote, Mohammad Bahram, Lu Kuang, Ting Li, Meng Wu, Yuji Jiang, Lu Luan, Muhammad Saleem, Franciska T. de Vries, Zhongpei Li, Baozhan Wang, Jiandong Jiang
Summary: Exploiting the potential benefits of plant-associated microbes can enhance crop productivity in a sustainable way. However, little is known about the biogeography and community structure of these microbes. This study constructs a database to analyze the global distribution of potential plant-beneficial bacteria (PBB) and shows that PBB diversity peaks in low-latitude regions. The distribution of potential PBB is primarily influenced by environmental filtering, mainly determined by local climate. Projections suggest that fossil-fuel-dependent scenarios could lead to a significant decline in PBB abundance by 2100, posing a potential threat to global food production and agroecosystem services.