Review
Ecology
Steven D. Warren, Roger Rosentreter, Nicole Pietrasiak
Summary: Biological soil crusts are composed of fungi, bacteria, algae, and bryophytes, which stabilize soil against erosion and are commonly found in arid and semiarid regions. These organisms play a crucial role in ecosystem and should be studied and managed to ensure their conservation.
RANGELAND ECOLOGY & MANAGEMENT
(2021)
Article
Microbiology
Rongliang Jia, Yanhong Gao, Lina Zhao, Tao Zhang, Hui Guo, Wanxue You, Yulong Duan
Summary: In this study, the influence of sand burial on bacterial and fungal communities inhabiting cyanobacterial and mixed crusts was assessed using a long-term field experiment and high-throughput sequencing. The results showed that sand burial treatment altered the diversity, abundance, and composition of the microbial communities. Different indicator taxa were identified in unburied and buried crusts, suggesting that changes in soil properties caused by sand burial may be a possible cause of changes in bacterial and fungal community composition in biological soil crusts.
Review
Ecology
Steven D. Warren
Summary: Microbes are commonly found in the atmosphere and terrestrial environments, playing significant ecological roles. They can travel through the air and participate in vital functions like condensation nuclei for precipitation.
FRONTIERS IN FORESTS AND GLOBAL CHANGE
(2022)
Review
Plant Sciences
Mateus Fernandes Oliveira, Adaises Simone Maciel-Silva
Summary: This review summarizes studies on biological soil crusts (BSCs) in Brazil, highlighting the importance of ecological, physiological, and taxonomic knowledge of these ecosystems. Comparisons with BSC communities in other parts of the world are made, and potential uses of BSCs in the colonization of other planets are proposed.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Review
Environmental Sciences
Aziz-Ur-Rahim Bacha, Iqra Nabi, Muhammad Zaheer, Wenbiao Jin, Lei Yang
Summary: Plastic waste has received significant research attention due to its accumulation, environmental issues, and impact on living organisms. There is an urgent need to remove plastic waste from the environment, and biodegradation is a promising treatment method. However, there is limited review on the bio-decomposition of plastics and the existing microbial species involved. This study provides an overview of influencing factors, existing species, and research gaps in biodegradation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Review
Engineering, Environmental
Pankaj Bhatt, Satish Chandra Pandey, Samiksha Joshi, Parul Chaudhary, Vinay Mohan Pathak, Yaohua Huang, Xiaozhen Wu, Zhe Zhou, Shaohua Chen
Summary: Growing human interference has led to an increase in both organic and inorganic contaminants, posing a threat to ecosystems. Removing these toxic pollutants from the environment is challenging. Bioremediation combined with nanotechnology shows promise as a cost-effective method for pollutant removal. Nanomaterials have exceptional properties, such as improved catalysis and adsorption, making them of great interest. By using microbial cultures and nanomaterials, the bioremediation of toxic compounds can be facilitated. Understanding the relationship between microorganisms, contaminants, and nanoparticles is crucial. This review focuses on the removal of toxic pollutants through the combined effects of nanoparticles and microbial technology, highlighting the significance and contribution of this novel nanobioremediation technique to sustainability.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Environmental Sciences
Shuo Li, Yalun Yang, Shanshan Yang, Heshan Zheng, Yongjie Zheng, M. Jun, Dillirani Nagarajan, Sunita Varjani, Jo-Shu Chang
Summary: Plastics have become an essential part of life, but when they enter the environment, they break down into smaller fragments called microplastics (MPs) which are detrimental to the environment and human health. Bioremediation is considered the most environmentally friendly and cost-effective method for MP degradation, but there is limited knowledge about it. This review explores the sources and migration behavior of MPs, discusses biodegradation potential and mechanisms, analyzes the factors influencing biodegradation, and discusses the prospects and challenges of biodegradation technologies for MPs.
Article
Engineering, Environmental
Xiaolin Kuang, Liang Peng, Ziyi Cheng, Siyan Zhou, Shaoning Chen, Cheng Peng, Huijuan Song, Changwu Li, Dan Li
Summary: Fertilization concentration significantly impacts the removal of Cd by paddy crusts. Low fertilizer concentration promotes Cd removal, while medium and high concentrations reduce Cd accumulation. Low concentration of fertilizer stimulates the growth of filamentous green algae, leading to an increase in the relative abundance of Pelagophyceae and Comamonadaceae. This study provides a new perspective for the remediation of heavy metal contamination in paddy fields.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Review
Environmental Sciences
Prateek Gururani, Pooja Bhatnagar, Vinod Kumar, Mikhail S. Vlaskin, Anatoly Grigorenko
Summary: Urbanization, industrialization and other human-related activities contribute to the discharge of toxic substances into the environment. The use of algae in wastewater treatment has been widely studied and it has been found that algae consortium systems are more effective than monocultures. Microorganisms such as bacteria or fungi in wastewater can form symbiotic relationships with algae, aiding in the removal of pollutants. This review explores the symbiotic relationships between algae and other microorganisms and their applications in wastewater treatment.
Article
Soil Science
Laibin Huang, Junhong Bai, Junjing Wang, Guangliang Zhang, Wei Wang, Xin Wang, Ling Zhang, Yaqi Wang, Xinhui Liu, Baoshan Cui
Summary: This study investigated the assembly processes of bacterial and fungal communities in the topsoil of a wetland transect in the Yellow River Estuary, China. The results showed that stochastic processes primarily shaped the two communities, with bacterial assembly being controlled by homogenizing dispersal and dispersal limitation, and fungal assembly being mostly regulated by undominated processes.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Review
Plant Sciences
Hyeon-Min Jeong, Henrietta Patterson, Philip Carella
Summary: This article introduces the pathosystems between non-vascular/non-seed bryophytes and microbes, discusses the conservation of core molecular aspects impacting plant infection and immunity across land plants, and highlights recent advances and future opportunities in the field of evolutionary molecular plant-microbe interactions.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Xin Zhou, Jinting Wang, Fang Liu, Junmin Liang, Peng Zhao, Clement K. M. Tsui, Lei Cai
Summary: This study found that the diversity of rhizosphere microbiota is negatively correlated with Fusarium wilt disease in tomato plants. Cross-kingdom SynComs showed the best suppression effect against the disease, providing a new effective strategy for controlling soil-borne diseases.
NATURE COMMUNICATIONS
(2022)
Review
Environmental Sciences
Aswin Thacharodi, Saqib Hassan, Tripti Singh, Ramkrishna Mandal, Jeganathan Chinnadurai, Hilal Ahmad Khan, Mir Ashiq Hussain, Kathirvel Brindhadevi, Arivalagan Pugazhendhi
Summary: PAHs, a class of organic priority pollutants, pose significant public health and environmental concerns due to their carcinogenic, genotoxic, mutagenic, and cytotoxic properties. With increased awareness of their negative effects on the environment and human health, research on eliminating PAHs from the environment has exponentially increased. Various environmental factors, such as nutrients, microorganisms present and their abundance, and the nature and chemical properties of PAHs, affect the biodegradation of PAHs. While bacteria and fungi have garnered the most attention for their biodegradation capacity, a comprehensive understanding of microbial communities and their enzymatic and biochemical properties is crucial for successful PAH degradation. This review aims to comprehensively discuss the latest findings and advancements in the microbial bioremediation of PAHs to enhance the broader understanding of PAHs bioremediation in the environment.
Review
Environmental Sciences
Esraa E. Ammar, Hadeer A. Rady, Ahmed M. Khattab, Mohamed H. Amer, Sohila A. Mohamed, Nour I. Elodamy, Ammar AL-Farga, Ahmed A. A. Aioub
Summary: Biofertilizers, extracted from a variety of living organisms, are ecofriendly techniques that can increase plant productivity by improving soil fertility and nutrient content. They offer a sustainable alternative to chemical fertilizers, avoiding pollution and heavy metal accumulation in soil. The use of biofertilizers promotes sustainable development in agriculture, mitigating climate change, and reducing the risk of diseases caused by pollution.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Ecology
Taylor L. Price, Jennifer Harper, Steven N. Francoeur, Halvor M. Halvorson, Kevin A. Kuehn
Summary: Research suggests that autotroph-heterotroph microbial interactions exert bottom-up controls on energy and nutrient transfer in aquatic detrital-based food webs. This study found that litter-associated algal and fungal production rates increased with higher nutrient and light availability, while microbial phosphorus absorption efficiency varied across diets.
Article
Plant Sciences
Diba A. Khan-Bureau, Saul Blanco, Eduardo A. Morales, Luc Ector, Michael S. Beauchene, Louise A. Lewis
Summary: This research used geometric morphometrics analysis to successfully distinguish between two populations of Didymosphenia in the Farmington River, Connecticut, and confirmed the identity of the second population as D. geminata. The study highlights the enhanced ability of geometric morphometrics, in combination with scanning electron microscopy and light microscopy, to differentiate between morphologically similar species of Didymosphenia.
EUROPEAN JOURNAL OF PHYCOLOGY
(2023)
Article
Evolutionary Biology
Nicole K. Reynolds, Jason E. Stajich, Gerald L. Benny, Kerrie Barry, Stephen Mondo, Kurt LaButti, Anna Lipzen, Chris Daum, Igor Grigoriev, Hsiao-Man Ho, Pedro W. Crous, Joseph W. Spatafora, Matthew E. Smith
Summary: Improved sequencing technologies have revolutionized the understanding of fungal diversity and evolution on a global scale. A study was conducted using low coverage genome sequencing (LCGS) to analyze 171 Kickxellomycotina fungi and obtain marker genes for phylogenomic reconstruction. The study aimed to evaluate the quality and utility of LCGS data, test relationships among different clades, and compare functional analyses to gain insights into trophic modes.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Xiuping Liu, Lu Lyu, Jiaqian Li, Biswarup Sen, Mohan Bai, Jason E. Stajich, Jackie L. Collier, Guangyi Wang
Summary: This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains and investigates their ecological functions from the perspective of organic matter degradation using comparative genomics and biochemical assays. The results show that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems and can actively participate in marine biochemical cycles as decomposers. The study also emphasizes the dual roles of endoglucanase in the process of cellulose degradation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Atul Munish Chander, Marcus de Melo Teixeira, Nitin K. Singh, Michael P. Williams, Anna C. Simpson, Namita Damle, Ceth W. Parker, Jason E. Stajich, Christopher E. Mason, Tamas Torok, Kasthuri Venkateswaran
Summary: NASA's spacecraft assembly facilities are monitored for the presence of bacteria or fungi that can survive in extraterrestrial environments. Fungi show diverse traits to adapt to extreme conditions, and their detection and eradication are necessary to prevent contamination of future missions. Three novel fungal strains were isolated from spacecraft assembly facilities during the Mars 2020 mission, and a polyphasic taxonomic approach supported the proposal for two new genera and one new species. These strains also exhibited unique resistance to ultraviolet-C and possessed specific biosynthetic gene clusters for metabolically active compounds.
Article
Ecology
Zsolt Merenyi, Krisztina Krizsan, Neha Sahu, Xiao-Bin Liu, Balazs Balint, Jason E. Stajich, Joseph W. Spatafora, Laszlo G. Nagy
Summary: Fungi are ecologically important heterotrophs that have evolved from a unicellular opisthokont ancestor to derived multicellular fungi. The genomes of 123 fungi and their relatives reveal the gradual loss of protist genes, major gene turnover, and duplication leading to the evolution of modern traits in filamentous fungi. The taxonomically defined Fungi represents a genomically non-uniform assemblage of species.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Chemistry, Multidisciplinary
Bo Yuan, Michelle F. Grau, Ramiro Mendonca Murata, Tamas Torok, Kasthuri Venkateswaran, Jason E. Stajich, Clay C. C. Wang
Summary: Aspergillus melleus IMV 01140, isolated from regions surrounding the Chernobyl nuclear power plant, produces neoaspergillic acid, which inhibits the growth of Candida albicans. However, large-scale production, isolation, and purification pose challenges.
Article
Microbiology
Tania Kurbessoian, Gretchen Heimlich-Villalta, Nichole Ginnan, Flavia Campos Vieira, Philippe E. Rolshausen, M. Caroline Roper, Jason E. Stajich
Summary: The genomes of eighteen Fusarium isolates from diseased and healthy citrus trees were sequenced and confirmed using single marker (TEF1-alpha) phylogenetic assessment. The study of traits and genotypes of plant-associated isolates is crucial for understanding the fungal contribution to citrus phytobiomes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Terrance Shea, Jason T. Mohabir, Tania Kurbessoian, Brittany Berdy, James Fontaine, Andreas Gnirke, Jonathan Livny, Jason E. Stajich, Christina A. Cuomo
Summary: Lichtheimia ornata is an emerging opportunistic Mucorales pathogen that causes fatal infections in immunocompromised individuals. Although environmentally acquired infections of this pathogen have been rarely reported, cases were recently identified in an analysis of COVID-19-associated mucormycosis in India. In this study, we present the annotated genome sequence of the environmental isolate CBS 291.66.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Evolutionary Biology
Julia N. Adams, Merly Escalona, Mohan P. A. Marimuthu, Colin W. Fairbairn, Eric Beraut, William Seligmann, Oanh Nguyen, Noravit Chumchim, Jason E. Stajich
Summary: Acarospora socialis, a pioneer species of ecological significance, has been understudied in terms of genomics. This study presents the first high-quality draft genome of A. socialis, which will be crucial for conservation efforts in California and understanding its adaptability to climate change.
JOURNAL OF HEREDITY
(2023)
Article
Mycology
Cassandra L. Ettinger, Talieh Ostovar, Mark Yacoub, Steven Ahrendt, Robert H. Hice, Brian A. Federici, Jason E. Stajich
Summary: Species of the phylum Blastocladiomycota, including the genus Coelomomyces, are understudied and little is known about their genomics. To address this, researchers generated draft-level genomes and annotations for C. lativittatus and demonstrated their utility in transcriptome analysis. They found that the C. lativittatus transcriptome is complex and dynamic, with differentially expressed genes and enriched GO terms across different life stages. The genomes and transcriptomes reported here provide valuable resources for understanding the biology of early-diverging fungal lineages.
Article
Microbiology
Daniel Murante, Elora G. Demers, Tania Kurbessoian, Marina Ruzic, Alix Ashare, Jason E. Stajich, Deborah A. Hogan
Summary: The identification of MRS4 mutations in Clavispora (Candida) lusitaniae and Exophiala dermatitidis in individuals with cystic fibrosis (CF) highlights a possible adaptive mechanism for fungi during chronic CF lung infections. The findings of this study suggest that loss of function of the mitochondrial iron transporter Mrs4 can lead to increased activity of iron acquisition mechanisms, which may be advantageous for fungi in iron-restricted environments during chronic infections. This study provides valuable information for researchers working toward a better understanding of the pathogenesis of chronic lung infections and more effective therapies to treat them.
Article
Genetics & Heredity
Tania Kurbessoian, Daniel Murante, Alex Crocker, Deborah A. Hogan, Jason E. Stajich
Summary: Individuals with cystic fibrosis are susceptible to chronic lung infections, some of which are caused by slow-growing yeast Exophiala dermatitidis. This study analyzed isolates of E. dermatitidis from two samples collected from the same subject 2 years apart. The isolates were highly similar and exhibited population heterogeneity at the phenotype and genomic levels.
G3-GENES GENOMES GENETICS
(2023)
Review
Microbiology
Andrii P. Gryganskyi, Jacob Golan, Anna Muszewska, Alexander Idnurm, Somayeh Dolatabadi, Stephen J. Mondo, Vira B. Kutovenko, Volodymyr O. Kutovenko, Michael T. Gajdeczka, Iryna M. Anishchenko, Julia Pawlowska, Ngoc Vinh Tran, Ingo Ebersberger, Kerstin Voigt, Yan Wang, Ying Chang, Teresa E. Pawlowska, Joseph Heitman, Rytas Vilgalys, Gregory Bonito, Gerald L. Benny, Matthew E. Smith, Nicole Reynolds, Timothy Y. James, Igor V. Grigoriev, Joseph W. Spatafora, Jason E. Stajich
Summary: The genome of Saccharomyces cerevisiae was the first eukaryotic organism genome sequenced, reported in 1996, but it took over 10 years to sequence any of the zygomycete fungi, which belong to the phyla Mucoromycota and Zoopagomycota. Over 1000 zygomycete genomes have now been sequenced, revealing deep phylogenetic separation between plant-associated saprotrophic Mucoromycota and animal-associated parasites and commensals in the Zoopagomycota. Genomic studies have provided insights into fungal adaptations to living on land, including light and gravity sensing, hyphal growth, and co-existence with terrestrial plants. Genomic data has also facilitated research on genome architecture, pathogenicity genes, secondary metabolites, and endosymbiotic bacteria and viruses.
Article
Microbiology
Kouka Hilaire Kabore, Abalo Itolou Kassankogno, Henri Adreit, Sebastien Ravel, Florian Charriat, Diariatou Diagne, Marc-Henri Lebrun, Didier Tharreau, Jason E. Stajich
Summary: Different fungal species within the Pleosporaceae family can infect rice and cause similar symptoms. Reference genomic sequences are valuable tools for studying the evolution of these species and developing accurate molecular diagnostic tools. In this study, we report the complete genome sequences of Bipolaris bicolor, Curvularia hawaiiensis, Curvularia spicifera, and Exserohilum rostratum.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Theo N. Kirkland, Sinem Beyhan, Jason E. Stajich
Summary: This study compares different gene prediction pipelines on the annotation of the Coccidioides immitis RS genome. Some genes originally predicted were not found in the other pipelines and these genes are more likely to be lineage-specific, poorly expressed, and have RNA-seq support for their structure. Genes predicted only by the Funannotate pipeline have lower functional annotations and expression levels. Genes predicted by multiple pipelines are more likely to have predicted functions and better expression.