Article
Agricultural Engineering
Jinsong Liang, Wei Fang, Qingyan Wang, Muhammad Zubair, Guangming Zhang, Weifang Ma, Yajing Cai, Panyue Zhang
Summary: Utilizing rumen microorganisms for anaerobic fermentation of corn straw to produce VFAs is important for biomass valorization, with VFA concentration reaching 8.99g/L within 72 hours. The bacterial and fungal community composition dynamically changed, but the core genera remained stable. Factors such as low pH and VFA accumulation had significant effects on bacterial and fungal communities.
BIORESOURCE TECHNOLOGY
(2021)
Article
Environmental Sciences
Hongbin Yan, Qi Zhang, Yunpu Wang, Xian Cui, Yuhuan Liu, Zhigang Yu, Shuming Xu, Roger Ruan
Summary: Microalgal biofilm cultivation using rice straw as carrier is a promising method for efficient microalgae production. The biomass productivity of unsterilized rice straw biofilm exceeds that of suspended culture. This study demonstrates the potential of using rice straw effectively as a carrier for microalgal biofilm, offering a new possibility for rice straw recycling.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Review
Microbiology
Ana Laura Totti Benatti, Maria de Lourdes Teixeira de Moraes Polizeli
Summary: Human population growth, industrialization, and globalization have caused severe climate and environmental crisis. Lignocellulolytic enzymes are proposed as a sustainable alternative to mitigate the impact of human activities on the environment. These enzymes can break down lignocellulosic biomass into different monomer units, enabling bioconversion into various products and applications in diverse industries.
Article
Environmental Sciences
Qinghui Liu, Cuihua Bai, Zhijun Zhang, Xueying Yin, Wanting Lin, Yinghui Huang, Lixian Yao
Summary: Rice straw incorporation can lead to arsenic methylation in soils, resulting in increased accumulation of methylated arsenic in rice plants and the emergence of rice straighthead disease. This study found that straw incorporation elevated the concentration of total and methylated arsenic in soils and rice plants, leading to decreased rice yield and the occurrence of straighthead disorder. Analysis of microbial communities revealed a reduction in abundance and diversity upon straw incorporation, with a notable increase in Rilcenellaceae, which was positively associated with methylated arsenic levels. These findings highlight the role of straw in shaping the soil microbial community and promoting arsenic methylation in soil, ultimately affecting rice uptake and causing straighthead disease.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Hoa Thai Doan, Phuong Thi Minh Nguyen, Thuy Thanh Tran, Thoa Kim Nguyen, Man Dinh Tran, Duc Ba Nguyen
Summary: This study focused on lime pretreatment of rice straw in northeast Vietnam for microbial lipid production, using a response surface methodology to optimize parameters. The optimal pretreatment conditions for maximal lipid yield were determined, with saturated, monounsaturated (MUFA), and polyunsaturated (PUFA) fatty acids composing the bio-lipid.
Article
Agronomy
Kailun Song, Shifei Liu, Guorong Ni, Qinlei Rong, Huajun Huang, Chunhuo Zhou, Xin Yin
Summary: Inoculating rumen microorganisms as inoculants can promote straw decomposition and returning to the field. The effects of soil moisture content on straw decomposition under rumen fluid-induced returning were investigated. The decomposition rate of straw showed a trend of first rising and then falling with an increase in soil moisture content. Treatments of 70% SMC with rumen fluid addition achieved the maximum rate of straw degradation. Rumen fluid favored the destruction of functional groups on the straw surface and the degradation of cellulose.
Article
Green & Sustainable Science & Technology
Fahad Al-Dhabaan
Summary: This study focused on utilizing an eco-friendly biodegradation technique to dispose of rice straw, which is a byproduct of rice cultivation. Actinobacteria isolated from cultivated soil and rhizosphere areas in Tabuk region played a crucial role in biodegrading starch, cellulose, lignin, and rice straw powder. One particularly effective actinobacterial isolate, identified as Streptomyces tendae, was able to significantly reduce the C/N ratio of rice straw within 42 days.
Article
Chemistry, Organic
Gregor Tegl, Peter Rahfeld, Katharina Ostmann, John Hanson, Stephen G. Withers
Summary: Functional screening of a metagenomic library derived from a human gut microbiome led to the identification of four active HexNAcase candidates belonging to CAZy family GH20, with the generation of two new thioglycoligases through detailed kinetic analysis. This work demonstrates the rapid development of useful glycoside-forming mutants of HexNAcases, diversifying the pool of biocatalysts for carbohydrate synthesis.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Plant Sciences
Wei Liu, Jichao Tang, Dahong Zhang, Xun Jiang, Bilin Lu, Wenjia Yang
Summary: This study investigated the effects of the co-application of straw-decomposing inoculants (SDIs) and ammonium bicarbonate on the decomposition rate of wheat straw, rice growth, and yield. The results showed that the co-application of SDIs and 30% ammonium bicarbonate can accelerate straw decomposition and increase rice growth and yield.
Article
Agricultural Engineering
Fengting Qu, Hanpeng Cheng, Ziyi Han, Zimin Wei, Caihong Song
Summary: The study aimed to understand the factors influencing the abundance of lignocellulose degrading enzyme genes during rice straw composting. Two strains, b4 (Bacillus subtilis) and z1 (Aspergillus fumigatus), were inoculated and three composting groups were established. Inoculation increased the abundance of lignocellulose degrading enzyme genes, promoting lignocellulose decomposition. Modular microorganisms, including Actinobacteria, Proteobacteria, Ascomycetes, and Basidiomycetes, were identified as driving factors influencing gene abundance. pH, organic matter, and soluble sugar content affected gene abundance by influencing the modular microorganisms. A potential priming effect was suggested based on these driving factors. This study provides theoretical guidance for enhancing lignocellulose degradation by regulating the abundance of lignocellulose degrading enzyme genes.
BIORESOURCE TECHNOLOGY
(2023)
Article
Engineering, Environmental
Leilei Fan, Fulin Sun, Zhihao Yang
Summary: This study used metagenomic sequencing to investigate the effects of chromium（Cr）and copper（Cu）on microbial communities and function. The results showed that high concentrations of Cr(VI) and Cu(II) reduced the removal efficiency of total nitrogen and ammonium. Different concentrations of Cr(VI) and Cu(II) led to significant changes in microbial communities and triggered specific response strategies. Additionally, enzymes of nitrogen metabolism pathway were found to have significant associations with corresponding bacteria.
JOURNAL OF WATER PROCESS ENGINEERING
(2022)
Article
Environmental Sciences
Ginevra Giangeri, Maria Silvia Morlino, Nicola De Bernardini, Mengyuan Ji, Matteo Bosaro, Valentina Pirillo, Paolo Antoniali, Gianluca Molla, Roberto Raga, Laura Treu, Stefano Campanaro
Summary: This study used an enrichment protocol to select microbial species involved in plastic degradation and investigated the metabolic pathways and microbial community evolution during the process. New enzymes related to plastic degradation were discovered, highlighting their significance in the degradation process.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Wenkai Yan, Yu Zhu, Wencheng Liu, Chengwu Zou, Bei Jia, Zhong-Qi Chen, Yanhong Han, Jianguo Wu, Dong-Lei Yang, Zhongkai Zhang, Lianhui Xie, Baoshan Chen, Rongbai Li, Shou-Wei Ding, Qingfa Wu, Zhongxin Guo
Summary: In this research, a new insect-borne positive-strand RNA virus called Rice tiller inhibition virus (RTIV) was discovered from Asian wild rice plants through metagenomic sequencing. It was demonstrated that RTIV can be transmitted by a specific species of aphids to cultivated rice and inhibit tillering. This discovery not only identified a rare aphid-transmitted viral pathogen of rice plants, but also highlighted the potential threat of novel pathogenic viruses spreading from native plants to important crop plants.
Article
Plant Sciences
You Liu, Yuan Yuan, Hui Yuan, Yan Wang, Chenzhong Jin, Hao Zhang, Jianliang Tang, Yihong Hu
Summary: The chalky part of hybrid rice seeds is susceptible to infection and poses risk to normal seeds during storage and soaking. Metagenomic shotgun sequencing was used to study seed-associated microorganisms in hybrid rice, and the results showed that fungi, specifically Rhizopus genus, were dominant. These fungal species could potentially be the pathogens in the chalky grains of hybrid rice seeds.
Article
Environmental Sciences
Sarmistha Sarangi, Harekrushna Swain, Totan Adak, Pratap Bhattacharyya, Arup K. Mukherjee, Gaurav Kumar, Sayaji T. Mehetre
Summary: Trichoderma-mediated rice straw management is an effective way to reduce straw burning, enrich soil fertility, and enhance intrinsic stress tolerance in rice plants.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Biodiversity Conservation
Caitlin D. Kuempel, Vivitskaia J. D. Tulloch, Alyssa L. Giffin, B. Alexander Simmons, Valerie Hagger, Carol Phua, Ove Hoegh-Guldberg
Summary: Conserving coral reefs is essential for maintaining marine biodiversity, protecting coastlines, and supporting livelihoods in coastal communities. Climate change poses a threat to coral reefs globally, but researchers have identified a group of coral reefs that are less exposed to climate impacts and strongly connected with other reef systems. By quantifying human impacts and creating management indices, countries can better manage local pressures on coral reefs and work towards a climate-ready future.
CONSERVATION BIOLOGY
(2022)
Article
Energy & Fuels
Mohammad Shahinur Rahaman, Sarttrawut Tulaphol, Md Anwar Hossain, Jacek B. Jasinski, Ning Sun, Anthe George, Blake A. Simmons, Thana Maihom, Mark Crocker, Noppadon Sathitsuksanoh
Summary: The study developed a dual acid phosphotungstic acid-encapsulated MOF catalyst for efficient conversion of biomass-derived glucose to 5-hydroxymethylfurfural. The catalyst design improved HMF selectivity and stability, providing insights for the design of new bifunctional solid acid catalysts.
Article
Biodiversity Conservation
Paul R. Elsen, Earl C. Saxon, B. Alexander Simmons, Michelle Ward, Brooke A. Williams, Hedley S. Grantham, Salit Kark, Noam Levin, Katharina-Victoria Perez-Hammerle, April E. Reside, James E. M. Watson
Summary: Rapid climate change is impacting biodiversity, ecosystem function, and human well-being, resulting in changes to the distribution of terrestrial life zones, with the pace of change accelerating. These changes have already had negative consequences for social and ecological systems.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Mood Mohan, Kaixuan Huang, Venkataramana R. Pidatala, Blake A. Simmons, Seema Singh, Kenneth L. Sale, John M. Gladden
Summary: The solubility parameter (SP) is crucial for indicating polarity and selecting solvents for dissolution. Recent studies have shown that ILs and DESs can efficiently solubilize lignocellulosic biomass for biofuel production. MD simulations are useful for predicting the solubility parameters of lignin, ILs, and DESs, and can be validated with experimental investigations. Additionally, the enthalpy of vaporization (Delta H-vap) of ILs/DESs is significantly higher than that of traditional organic solvents.
Article
Biology
Jane Khudyakov, Rachel R. Holser, Craig A. Vierra, Serena T. Ly, Theron K. Niel, Basma M. Hasan, Daniel E. Crocker, Daniel P. Costa
Summary: Northern elephant seals undergo prolonged fasting during energy-intensive life-history stages and display unique metabolic features. Changes in apolipoprotein composition may play a role in maintaining high HDL levels in these seals.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hemant Choudhary, Venkataramana R. Pidatala, Mood Mohan, Blake A. Simmons, John M. Gladden, Seema Singh
Summary: This study reports the synthesis of three unique Schiff-base ionic liquids derived from lignin for the purpose of replacing fossil-derived chemicals. The synthesized ionic liquids were evaluated using analytical and computational tools, with the ones containing only imines showing the best performance.
Article
Chemistry, Multidisciplinary
Ezinne C. Achinivu, Mica Cabrera, Athiyya Umar, Minliang Yang, Nawa Raj Baral, Corinne D. Scown, Blake A. Simmons, John M. Gladden
Summary: Ionic liquids (ILs) are versatile solvents used in various industries, but their high cost limits commercialization. This study developed a simple and cost-effective method to synthesize protic ionic liquids (PILs) in situ for biomass pretreatment, demonstrating economic advantages and environmental efficiency.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
Article
Microbiology
Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik Scheller, Blake A. Simmons, Javier A. Ceja-Navarro, Steven W. Singer
Summary: In this study, microbiomes cultivated on sorghum were used to assess their performance in deconstructing plant cell walls. Network reconstructions and functional analysis revealed the importance of cellulose-degrading Actinobacteria in differentiating the performance of these microbiomes.
Article
Agronomy
Virginie Perlo, Agnelo Furtado, Frederik C. Botha, Gabriel R. A. Margarido, Katrina Hodgson-Kratky, Hemant Choudhary, John Gladden, Blake Simmons, Robert J. Henry
Summary: This study used multi-omics correlation analysis to investigate the metabolic pathways and critical genes involved in sugarcane development. Chemical and metabolome analysis showed an increase in lignin, sucrose, carbon, and certain amino acids during culm development. Transcriptome analysis revealed different functionalities and activities during different developmental stages.
FOOD AND ENERGY SECURITY
(2022)
Article
Biochemical Research Methods
Kai Deng, Xi Wang, Nicole Ing, Paul Opgenorth, Markus de Raad, Jinho Kim, Blake A. Simmons, Paul D. Adams, Anup K. Singh, Taek Soon Lee, Trent R. Northen
Summary: We developed a novel mass spectrometry-based assay that allows rapid quantification of primary alcohols produced by cell cultures. This assay combines TEMPO-based oxidation chemistry and oxime ligation, followed by product analysis using Nanostructure-Initiator Mass Spectrometry. It can accurately monitor C5 to C18 alcohols, as well as glucose and gluconate in the growth medium, which is crucial for strain characterization and optimization. The assay shows comparable results to gas chromatography for isoprenol production but requires significantly less acquisition time per sample. By applying this assay, we gained new insights into the utilization of alcohols by P. Putida and found that this strain had limited growth on heptanol and octanol.
ANALYTICAL BIOCHEMISTRY
(2023)
Review
Biochemical Research Methods
Hector G. Martin, Tijana Radivojevic, Jeremy Zucker, Kristofer Bouchard, Jess Sustarich, Sean Peisert, Dan Arnold, Nathan Hillson, Gyorgy Babnigg, Jose M. Marti, Christopher J. Mungall, Gregg Beckham, Lucas Waldburger, James Carothers, ShivShankar Sundaram, Deb Agarwal, Blake A. Simmons, Tyler Backman, Deepanwita Banerjee, Deepti Tanjore, Lavanya Ramakrishnan, Anup Singh
Summary: Self-driving labs combine fully automated experiments with AI, bringing a new paradigm to scientific research. While there are functioning SDLs in chemistry and materials science, synthetic biology offers unique opportunities due to the genome as a single target for affecting biological cell behavior. However, investment in biological SDLs should be directed towards solving difficult and enabling biological questions. Here, challenges and opportunities in creating SDLs for synthetic biology are discussed.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Microbiology
Mee-Rye Park, Rahul Gauttam, Bonnie Fong, Yan Chen, Hyun Gyu Lim, Adam M. Feist, Aindrila Mukhopadhyay, Christopher J. Petzold, Blake A. Simmons, Steven W. Singer
Summary: The study of pentose sugar catabolism in the P. putida group revealed inherent diversity, which provides alternative hosts for biomass conversion.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Julius Choi, Alberto Rodriguez, Blake A. A. Simmons, John M. M. Gladden
Summary: The range of applications for industrial hemp has expanded in various sectors. Hemp hurd can be used to produce biodegradable packaging materials, which can then be used as a feedstock for biofuel production. The packaging materials showed better performance compared to untreated hemp hurd in terms of sugar yield and sugar concentrations. This study demonstrates the potential of valorizing hemp hurd-based packaging as a feedstock for biofuel production once it reaches its end of primary use.
Article
Multidisciplinary Sciences
Mood Mohan, Blake A. Simmons, Kenneth L. Sale, Seema Singh
Summary: Lignin, a abundant biopolymer in nature, has the potential to be used as sustainable fuels, chemicals, and materials. However, finding suitable solvents and efficient technologies for lignin dissolution and depolymerization is a challenge. Based on computational modeling and molecular dynamics simulations, certain ionic liquids, such as tetrabutylammonium-based ILs, are predicted to be effective solvents for lignin dissolution.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Vanessa Brisson, Courtney Swink, Jeffrey Kimbrel, Xavier Mayali, Ty Samo, Suzanne M. Kosina, Michael Thelen, Trent R. Northen, Rhona K. Stuart
Summary: The roles of different ecological classes of algal exometabolites in regulating microbial community composition are not well understood. In this study, we identified exometabolites from the diatom Phaeodactylum tricornutum and investigated their potential to influence bacterial abundances. We found that secretion of selective bacterial growth substrates represents one mechanism by which algal exometabolites can modulate bacterial community composition.
