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Preprint ARTICLE | doi:10.20944/preprints202309.1359.v1

Untangling the Distribution of Encephalartos villosus in Nutrient Deficient Soils of South Africa

Nqobile Mostsomane, Terence Nkwanwir Suinyuy, María A. Pérez-Fernández, Anathi Magadlela

Subject: Environmental And Earth Sciences, Ecology Keywords: Encephalartos villosus; cycad-microbe symbiosis; nutrient deficient soils; biological nitrogen fixation

Online: 20 September 2023 (13:55:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0366.v1

The Natal Giant Cycad (Encephalartos natalensis) Associated Nutrient-cycling Microbes and Enzymes Contribute to Soil Nutrient Inputs and Persistence in Nutrient-poor Disturbed Savanna Woodland Ecosystems

Siphelele Ndlovu, Terrence N. Suinyuy, María Pérez-Fernández, Anathi Magadlela

Subject: Biology And Life Sciences, Plant Sciences Keywords: Encephalartos natalensis; microbe-symbiosis; soil nutrition; enzyme activities; soil nutrient cycling

Online: 19 January 2023 (15:29:52 CET)

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Preprint ARTICLE | doi:10.20944/preprints202012.0391.v1

Msh Pilus Mutations Increase the Ability of a Free-Living Bacterium to Colonize a Piscine Host

Jarrett F. Lebov, Brendan J. M. Bohannan

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Host-microbe; Zebrafish; Shewanella; Symbiosis; Microbial evolution; Msh pilus; Adaptation; Biofilms; Fitness; Colonization

Online: 15 December 2020 (16:34:25 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.1031.v1

Genomic and Transcriptomic Analysis of Pea (Pisum sativum L.) Breeding Line ‘Triumph’ with High Symbiotic Responsivity

Evgeny A. Zorin, Anton S. Sulima, Aleksandr I. Zhernakov, Daria O. Kuzmina, Valeria A. Rakova, Marina S. Kliukova, Daria A. Romanyuk, Olga A. Kulaeva, Gulnara A. Akhtemova, Oksana Y. Shtark, Igor A. Tikhonovich, Vladimir A. Zhukov

Subject: Biology And Life Sciences, Plant Sciences Keywords: plant-microbe symbiosis; legumes; Pisum sativum; symbiotic responsivity; genomics; transcriptomics; differential gene expression; molecular breeding

Online: 15 November 2023 (15:49:19 CET)

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Preprint REVIEW | doi:10.20944/preprints202404.1475.v1

Integrated Benefits to Agriculture with Trichoderma and Other Endophytic Microbes

GARY E Harman

Subject: Agricultural Science And Agronomy, Biology And Life Sciences Keywords: holobiont, plant-microbe interactions, biocontrol

Online: 23 April 2024 (11:28:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1720.v1

Fungal-Algal Association Drives Lichen Mutualistic Symbiosis: A Case Study With Trebouxia-Related Lichens

Ya-Bo Zuo, Da-Yong Han, Yan-Yan Wang, Qiu-Xia Yang, Qiang Ren, Xin-Zhan Liu, Xin-Li Wei

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Trebouxia; lichen; symbiosis; association; coevolution

Online: 25 May 2023 (03:09:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202211.0231.v1

Establishment of the Bacterial Microbiota in A Lab-Reared Model Teleost Fish, the Medaka Oryzias Latipes

Charlotte Duval, Benjamin Marie, Pierre Foucault, Sébastien Duperron

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Microbiota; Ecotoxicology; Symbiosis acquisition; Holobiont

Online: 14 November 2022 (02:40:58 CET)

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Preprint REVIEW | doi:10.20944/preprints202206.0284.v1

Building Consensus around the Assessment and Interpretation of Symbiodiniaceae Diversity

Sarah Davies, Matthew H. Gamache, Lauren I. Howe-Kerr, Nicola G. Kriefall, Andrew C. Baker, Anastazia T. Banaszak, Line K. Bay, Anthony J. Bellantuono, Debashish Bhattacharya, Cheong Xin Chan, Danielle C. Claar, Mary Alice Coffroth, Ross Cunning, Simon K. Davy, Javier del Campo, Erika M. Diaz-Almeyda, Jorg C. Frommlet, Lauren E. Fuess, Raul A. Gonzalez-Pech, Tamar L. Goulet, Kenneth D. Hoadley, Emily J. Howells, Benjamin C. C. Hume, Dustin W. Kemp, Carly, D. Kenkel, Sheila A. Kitchen, Todd C. LaJeunesse, Senjie Lin, Shelby McIlroy, Ryan McMinds, Matthew R. Nitschke, Clinton A. Oakley, Raquel S. Peixoto, Carlos Prada, Hollie M. Putnam, Kate Quigley, Hannah G. Reich, James Davis Reimer, Mauricio Rodriguez-Lanetty, Stephanie Rosalas, Osama S. Saad, Eugenia M. Sampayo, Scott Santos, Eiichi Shoguchi, Edward G. Smith, Michael Stat, Timothy G. Stephens, Marie E. Strader, David J. Suggett, Timothy D. Swain, Cawa Tran, Nikki Traylor-Knowles, Christian R. Voolstra, Mark E. Warner, Virginia M. Weis, Rachel Wright, Tingting Xiang, Hiroshi Yamashita, Maren Ziegler, Adrienne M.S. Correa, John Everett Parkinson

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Symbiodinaceae; genetic diversity; coral symbiosis

Online: 21 June 2022 (04:49:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0358.v1

Effects of Bradyrhizobium japonicum on Nitrogen Content in Soybean Leaves and Seeds Cultivated on Acidic Soils

Ben Tshibuyi Kasu-Bandi, Fabien Kitengie Kitengie, Jonas Lwamuguma Bagaluza, Aristote Bwende Nkolomini, Emery Kasongo Lenge, Antoine Kanyenga Lubobo

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Symbiosis; rhizobium; Ferralsol; Haut-Katanga

Online: 17 August 2021 (10:16:48 CEST)

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Preprint REVIEW | doi:10.20944/preprints202104.0682.v1

Molecular Models of Wolbachia-Induced Cytoplasmic Incompatibility Must Account for the Multiplicity of Compatibility Types.

Alice Namias, Mathieu Sicard, Mylène Weill, Sylvain Charlat

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Wolbachia; toxin-antidote; Culex; Drosophila; symbiosis

Online: 26 April 2021 (15:56:50 CEST)

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Working Paper REVIEW

Microbiome-Aware Ecotoxicology of Organisms: Relevance, Pitfalls and Challenges

Sébastien Duperron, Sébastien Halary, Alison Gallet, Benjamin Marie

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: toxicology; microbiota; symbiosis; contaminants; resilience; environment

Online: 8 August 2020 (05:01:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.1852.v1

Dietary Serine Supplementation Improves Growth Performance, Meat Quality, and Composition of Gut Microbes and Metabolites in Growing‐Finishing Pigs

Guo Yiting, He Fang, Deng Zhiying, Yin Jie, Guan Guiping, Xie Zhengjun, Zhou Xihong

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Finishing pig; Gut microbe; Meat quality; Metabolite; Serine

Online: 25 December 2023 (13:16:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202211.0521.v1

Comparative Transcriptomics Profiling of Perennial Ryegrass Infected with Wild Type or a ∆velA Epichloë Festucae Mutant Reveals Host Processes Underlying Mutualistic versus Antagonistic Interactions

Mostafa Rahnama, Paul Maclean, Damien J. Fleetwood, Richard D. Johnson

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: plant–microbe interactions; endophytes; comparative transcriptomics; velvet genes

Online: 29 November 2022 (02:06:31 CET)

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Preprint REVIEW | doi:10.20944/preprints202312.1617.v1

Cladosporium - Insect Relationships

Rosario Nicoletti, Elia Russo, Andrea Becchimanzi

Subject: Biology And Life Sciences, Plant Sciences Keywords: Cladosporiaceae; endophytes; entomopathogens; mycophagy; symbiosis; species complexes

Online: 21 December 2023 (06:10:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0339.v1

Proteomic Profiling and Rhizosphere-Associated Microbial Communities Reveal Adaptive Mechanisms of Dioclea Apurensis Kunth in Eastern Amazon’s Rehabilitating Minelands

Sidney Vasconcelos do Nascimento, Paulo Henrique de Oliveira Costa, Hector Herrera, Cecilio Frois Caldeira, Markus Gastauer, Silvio Junio Ramos, Guilherme Oliveira, Rafael Borges da Silva Valadares

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: abiotic stress; proteomic; rehabilitating minelands; rhizosphere; symbiosis

Online: 24 January 2022 (10:07:29 CET)

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Preprint ARTICLE | doi:10.20944/preprints201710.0123.v1

Gene Silencing of Argonaute5 Negatively Affects the Establishment of the Legume-Rhizobia Symbiosis

Maria del Rocio Reyero-Saavedra, Zhenzhen Qiao, María del Socorro Sánchez-Correa, M. Enrique Díaz-Pineda, Jose L. Reyes, Alejandra A. Covarrubias, Marc Libault, Oswaldo Valdés-López

Subject: Biology And Life Sciences, Plant Sciences Keywords: common bean; soybean; Argonaute5; legume-rhizobia symbiosis

Online: 18 October 2017 (03:20:37 CEST)

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Preprint REVIEW | doi:10.20944/preprints202311.1515.v1

Environmental and Ecological Impacts of Acid Mine Drainage, Using Microbes to Mitigate Its Effects

Adejide Adewoyin, Itunu Adewoye

Subject: Environmental And Earth Sciences, Waste Management And Disposal Keywords: Acid Mine Drainage; Remediation; Heavy metals; microbe; Environmental effects

Online: 23 November 2023 (11:07:28 CET)

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Preprint REVIEW | doi:10.20944/preprints202306.1042.v1

Importance of Omics Approaches in Plant-Microbe Interactions in Plant Disease Control

Ramlal Ayyagari, Anita Rani, Aparna Nautiyal, Charu Kalra, Reeta Kumari, Jitendra Kumar, Shivamurthy Veeranna, Vachaspati Mishra

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Crop improvement; Omics, Pathogenesis; Plant-microbe interactions (PPI); Resistance

Online: 14 June 2023 (10:09:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0902.v1

Mucosal Metabolomic Signatures in Chronic Colitis: Novel Insights into the Pathophysiology of Inflammatory Bowel Disease

Nathan Calzadilla, Aisha Qazi, Anchal Sharma, Kai Mongan, Shane Comiskey, Jahnavi Manne, Alvin G. Youkhana, Sonam Khanna, Seema Saksena, Pradeep K. Dudeja, Waddah A. Alrefai, Ravinder K. Gill

Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: chronic colitis; mucosal inflammation; host-microbe interactions; mucosal metabolomics

Online: 13 June 2023 (08:39:45 CEST)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202104.0743.v1

The Misleading History of VIRUSes

Francisco Prosdocimi, Savio Farias, Juliana Cortines, Marco José

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: origin of life; virus; evolution; symbiosis; progenotes; fuca;

Online: 28 April 2021 (10:28:30 CEST)

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Viruses were classically named after the very same Latin word virus, originally meaning poison or venom. Public understanding of viruses reinforces their “malign” aspects, especially nowadays under the COVID-19 global pandemic. It is our aim here to propose a new way to view viruses and understand their origins and evolution. First, viruses are the most abundant biological systems found on Earth. They can be found almost everywhere and form a subtle biological layer named virosphere. Second, viruses are probably the most important drivers of molecular evolution and they are active agents of ecosystems maintenance and homeostasis, allowing and driving their dynamic modification. A significant number of eukaryotic genomes are composed by genome elements similar to viruses and these endogenous viruses are continuously acting for our equilibrium and fitness. They are responsible for the origin of species-specific orphan genes that allow adaptation through the development of specific traits in separate lineages of eukaryotes. Accumulated evidence indicate that a viral infection was responsible to create the eukaryotic nucleus and, also, it is a syncytium structure caused by viral replication that allows the formation of the placenta. Therefore, viruses were fundamental for the evolutionary fate of eukaryotes and mammals. The presence of virus-specific genes that are absent in cellular organisms indicates that viruses existed before cells. Besides, such as progenotes, viruses are simply ribonucleoproteic entities and their capsids are orders of magnitude simpler than proteolipidic membranes. Here, we (i) propose a complete scenario to describe the major transitions in prebiotic evolution, (ii) present the possibility that viruses emerged before LUCA, and (iii) suggest that viruses originated at the age of progenotes. However, viruses do not form a monophyletic clade. They should be seen as an evolutionary stable strategy recurrently achieved by biological systems to survive. We propose that the word “VIRUS”, known as venom, is historically mistaken and introduce a new interpretation for their name as an acronym for “Very Important Replicator Unit and Symbiont”. But more than being “very important”, viruses are of “Utmost” relevance for the maintenance of life in biosphere, by which reason we suggest referring to them as “UIRUS” to reinforce their incredible role in symbiosis and their beneficial characteristics over the infectious ones.

Preprint ARTICLE | doi:10.20944/preprints201709.0062.v3

Strong Cognitive Symbiosis: Cognitive Computing for Humans

Csaba Veres

Subject: Computer Science And Mathematics, Information Systems Keywords: cognitive computing; cognition; AI; cognitive symbiosis; language; HCI

Online: 2 November 2017 (03:35:19 CET)

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Preprint REVIEW | doi:10.20944/preprints202402.0924.v1

Unveiling the Hidden Messengers: Exploring the Role of Extracellular Vesicles in Plant-Microbe Interactions

Sarita Pandey, Anaïs Blache, Wafa Achouak

Subject: Environmental And Earth Sciences, Environmental Science Keywords: extracellular vesicles; plant-microbe interactions; plant defense mechanisms; interkingdom communication

Online: 18 February 2024 (11:48:29 CET)

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Preprint REVIEW | doi:10.20944/preprints202310.0050.v1

Unleashing the Power of Beneficial Microorganisms for Advancing Crop Improvement: An In-depth Review

Godswill Ntsomboh Ntsefong, Gabriel Mahbou Somo Toukam, Kingsley Tabi Mbi, Seyum Essubalew Getachew, Aoudou Yaouba, Shariati Mohammad Ali, Tonjock Rosemary Kinge, Gerald Ngo Teke

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Beneficial microorganisms, Crop improvement, Plant-microbe interactions, Biofertilizers, Symbiotic relationships

Online: 2 October 2023 (11:12:30 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.1772.v1

The Role of Nutrients in Plant and Herbivore Interactions

Ming Zeng

Subject: Biology And Life Sciences, Plant Sciences Keywords: microbe-plant-herbivore interactions; nutrients; resistance; tolerance; soil; mycorrhiza; rhizobia

Online: 25 August 2023 (07:12:35 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.1575.v1

Nitrogen Journey in Plants: from Uptake to Metabolism to Stress response and Microbe Interaction

Omar Zayed, Omar A Hewedy, Ali Abdelmoteleb, Mohammed Ali, Mohamed S.G Youssef, Ahmed F Roumia, Danelle Seymour, Ze-Chun Yuan

Subject: Biology And Life Sciences, Plant Sciences Keywords: Nitrogen uptake; nitrogen metabolism; plant stress response; plant-microbe interaction

Online: 23 August 2023 (05:24:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0113.v1

Functional Diversity of Microbial Communities in the Soybean (Glycine max L.) Rhizosphere from Free State, South Africa

Titilope Tinu Ajiboye, Ayansina Segun Ayangbenro, Olubukola Oluranti Babalola

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: microbial communities; plant-microbe interractions; rhizodeposition; SEED subsystem; shotgun metagenomics

Online: 7 July 2022 (06:05:13 CEST)

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Preprint REVIEW | doi:10.20944/preprints202207.0306.v2

Help Me, Symbionts, You’re My Only Hope: Approaches to Accelerate Our Understanding of Coral Holobiont Interactions

Colleen Bove, Maria Valadez Ingersoll, Sarah Davies

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Coral symbiosis; immunity; microbiome; global change; coral holobiont; Symbiodiniaceae

Online: 14 September 2022 (15:33:09 CEST)

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Preprint REVIEW | doi:10.20944/preprints202008.0350.v2

Symbiont-mediated Cytoplasmic Incompatibility:What Have We Learned in 50 years?

J. Dylan Shropshire, Brittany Leigh, Seth R. Bordenstein

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: cytoplasmic incompatibility; Wolbachia, prophage WO; CifA and CifB; symbiosis

Online: 11 September 2020 (06:27:07 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints201912.0046.v1

A Hypothesis of Symbiosis between Humans and Poliovirus as a Critical Evolutionary Step in Human Speciation

Adnan Saeed Amin

Subject: Biology And Life Sciences, Virology Keywords: symbiosis; speciation; humans; polio; CD155; PVR; evolution; ASD; autism

Online: 4 December 2019 (11:09:42 CET)

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Preprint ARTICLE | doi:10.20944/preprints201908.0318.v1

Epistemological and Ethical Implications of the Free Energy Principle

Eray Özkural

Subject: Computer Science And Mathematics, Computer Science Keywords: AI; ethics; safety; autonomy; free energy principle; reductionism; symbiosis

Online: 30 August 2019 (07:42:42 CEST)

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The free energy principle states that self-organization occurs through minimization of free energy, which is a measure of potential thermodynamic work. By minimizing free energy, the organism happens to also minimize surprise over its boundary, promoting chances of survival. We discuss the ethical implications of the cognitive goal in detail from an empirical point of view, highlighting the principle of least action as a physical basis of Occam's razor, the universality of the free energy principle, and its explanation of natural selection. We explain that the free energy principle extends to groups of organisms and helps us understand group-scale adaptations and selection in biology. The free energy principle applies to all scales of organization in the organism from single cells to the entire nervous system. When this principle is taken to its logical extremes of modeling groups, populations and ecosystems, we uncover a new, evolutionarily sensible path at explaining puzzling aspects of human motivation and judgement, including ethical decisions. To minimize free energy, populations have to act to maximize gathering of information, while building effective models at mitigating changes to its dynamic structure. The free energy principle thus provides a naturalistic explanation of some of our deepest ethical intuitions, and valuable principles of social behavior. We interpret the cognitive goal that corresponds to the principle as seeking a dynamic, fruitful, yet peaceful activity that sustains the organism. This state of mind is interestingly similar to the Buddhist intuition of mental equanimity; the organism's final goal is to be at peace and harmony with the environment. Another immediately relevant aspect is that assemblies must form to promote symbiotic, synergistic, positive feedback loops, which coincides with the findings of ecologists. Therefore, ethics naturally emerges in self-organizing systems. Assemblies of organisms must ultimately unite in macro-minds to achieve the greatest reduction in free energy, as well as building technological extensions of themselves to improve their capacity to do such, therefore the principle also predicts a post-singularity world-mind composed mostly of artificial intelligence.

Preprint REVIEW | doi:10.20944/preprints202307.0451.v1

Communication between Plants and Rhizosphere Microbiome: Exploring the Root Microbiome for Sustainable Agriculture

Ben Jesuorsemwen Enagbonma, Fadiji Emmanuel Ayomide, Ayansina Segun Ayangbenro, Olubukola Oluranti Babalola

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: plant-microbe interactions, signaling molecule, root exudate, disease suppression, crop production

Online: 7 July 2023 (08:33:10 CEST)

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Preprint REVIEW | doi:10.20944/preprints202211.0255.v3

How Much of Aging Is Simply a Trash Collection Problem?

Michael Renteln

Subject: Biology And Life Sciences, Aging Keywords: Anti-aging therapy; lipofuscin; SENS; oncolytic vector; telomerase; TFEB; intracellular microbe

Online: 22 February 2023 (15:24:21 CET)

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Preprint REVIEW | doi:10.20944/preprints202208.0229.v5

Lipofuscin as the Main Driving Force of Current Age-Related Disease: Justification and Strategies for Removal

Michael Renteln

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Anti-aging therapy; lipofuscin; SENS; TFEB; intracellular microbe; and synthetic chemotaxis

Online: 2 November 2022 (03:41:32 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0076.v1

Microbes in the Datura Rootzone Contribute to an Antioxidant Support System of Flavonoids and Other Aromatic Compounds

Savanah Senn, Kelly Pangell, Adrianna L. Bowerman

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Weed science; Plant-microbe interactions; Medicinal plants; shotgun metagenomics; soil metabarcoding

Online: 3 November 2021 (09:19:12 CET)

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Preprint ARTICLE | doi:10.20944/preprints202209.0345.v1

The Root Proteomes of Mimosa acutistipula Provide Insights into the Stress Response Mechanisms in Plants Grown in Native Ecosystems and Eastern Amazon's Rehabilitating Minelands

Sidney Vasconcelos do Nascimento, Héctor Herrera, Paulo Henrique de Oliveira Costa, Felipe Costa Trindade, Isa Rebeca Chagas Da Costa, Cecilio Frois Caldeira, Markus Gastauer, Silvio Junio Ramos, Guilherme Oliveira, Rafael Borges Da Silva Valadares

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Abiotic Stress; Amazon; Canga; Iron mining; Mineland Rehabilitation; Proteomics; Symbiosis

Online: 22 September 2022 (13:34:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0207.v1

Phosphate Deficiency Negatively Affects Early Steps of the Symbiosis between Common Bean and Rhizobia

Mariel C Isidra-Arellano, María del Rocio Reyero-Saavedra, María del Socorro Sánchez-Correa, Lise Pingault, Sidharth Sen, Trupti Joshi, Lourdes Girard, Norma A Castro-Guerrero, David G Mendoza-Cozatl, Marc Libault, Oswaldo Valdés-López

Subject: Biology And Life Sciences, Plant Sciences Keywords: Phosphorus deficiency, common bean, rhizobia, molecular dialog, symbiosis, gene transcription

Online: 12 September 2018 (01:29:38 CEST)

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Working Paper ARTICLE

The Influence of Transplanted Trees on Soil Microbial Diversity in Areas Affected by Coal Mining Subsidence of the Loess Plateau in China

Yangnan Guo, Xianghong Liu, Borjigin Tsolmon, Jin Chen, Wei Wei, Shaogang Lei, Junzhe Yang, Yuying Bao

Subject: Environmental And Earth Sciences, Environmental Science Keywords: transplanted trees; soil microbe diversity; coal mining subsidence areas; the loess plateau

Online: 23 September 2019 (00:44:51 CEST)

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Soil microbial diversity in areas affected by coal mining subsidence is closely associated with vegetation restoration. In this study, we compared the diversity of soil bacteria and fungi under different vegetation restoration modes in the subsidized Daliuta coal mining region in western China. The dominant bacteria, Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria, were found at abundances of 29.43–34.68%, 15.87–24.75%, 13.09–19%, and 12.06–15.36%, respectively. The dominant fungi, Ascomycetes and Zygomycetes, had abundances of 23.96–71.08% and 10.42–56.26%, respectively. The diversity indices (Sobs, Shannon, and Chao1) of the rhizosphere soil bacteria and fungi were significantly lower in the primary Stipa breviflora phytocommunity than in the phytocommunities of transplanted trees. Among physicochemical soil parameters, total nitrogen (TN), total phosphorus (TP), water content (WC), and pH affected soil bacterial diversity, and available phosphorus (AP) and TN affected bacterial community structure the most. Furthermore, WC affected soil fungal diversity, whereas TP and TN mostly affected the fungal community structure. However, edaphic factors did not uniformly affect all microbial groups. Although TN, WC, and AP significantly influenced the species richness of Actinobacteria and Proteobacteria (p<0.05), TP was significantly negatively correlated with species richness in Acomycota, Basidiomycota, and Zygomycota (p<0.05). However, TN influenced the species richness of Zygomycota (p<0.05) . Furthermore, we found that the rhizosphere microbial diversity of the CK phytocommunity differed from that of the transplanted tree communities in the study area; i.e., the transplanted trees promoted soil microbial diversity in phytocommunities, and moreover, different edaphic factors varied in their effect on the community composition of rhizosphere bacteria and fungi. We will continue to monitor the soil microbial diversity in the study area with the goal to provide guidance for environmental remediation of areas affected by coal mining subsidence.

Preprint ARTICLE | doi:10.20944/preprints201710.0122.v1

Dynamics of the Bacterial Community Associated with Phaeodactylum tricornutum Cultures

Fiona Wanjiku Moejes, Ovidiu Popa, Antonella Succurro, Julie Maguire, Oliver Ebenhöh

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: microbial communities; host-microbe interactions; mathematical modelling; diatoms; synthetic ecology; algal biotechnology

Online: 17 October 2017 (17:37:49 CEST)

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Preprint REVIEW | doi:10.20944/preprints202402.1287.v1

Endophytic Fungi for Crops Adaptation to Abiotic Stresses

Adan Topiltzin Morales-Vargas, Varinia López-Ramírez, Cesar Alvarez-Mejia, Juan Vázquez-Martínez

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Endophytic fungi; Abiotic stress; Crop adaptation; Symbiosis; Agricultural sustainability; Climate change.

Online: 22 February 2024 (08:55:32 CET)

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Preprint ARTICLE | doi:10.20944/preprints202210.0173.v1

A New Albomycin-Producing Strain of Streptomyces globisporus Subsp. globisporus May Provide Protection for Ants Messor structor

Yuliya V. Zakalyukina, Nikolay A. Pavlov, Dmitrii A. Lukianov, Mikhail V. Biryukov, Valeria I. Marina, Olga A. Belozerova, Vadim N. Tashlitsky, Elena B. Guglya, Ilya A. Osterman

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: actinobacteria; Streptomyces globisporus subsp. globisporus; albomycin; defensive symbiosis; ants; Messor structor

Online: 12 October 2022 (10:24:10 CEST)

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Preprint REVIEW | doi:10.20944/preprints202206.0030.v1

New Insights into the Boron Essentiality on Humans and Animals

Andrei Bita, Ion Romulus Scorei, Tudor Adrian Balseanu, Maria Viorica Ciocilteu, Antonia Radu, George Dan Mogosanu, Steven A. Benner

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: naturally organic boron containing compounds; prebiotic candidate; microbiome; intestinal microflora; symbiosis

Online: 2 June 2022 (09:04:15 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0172.v2

Trends in Symbiont-Induced Host Cellular Differentiation

Shelbi Russell, Jennie Ruelas Castillo

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: Wolbachia; Drosophila; Symbiosis; Cellular microbiology; Cellular differentiation; Epigenetics; Transcription; Translation; Proteolysis

Online: 28 April 2020 (09:18:03 CEST)

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Bacteria participate in a wide diversity of symbiotic associations with eukaryotic hosts that require precise interactions for bacterial recognition and persistence. Most commonly, host-associated bacteria interfere with host gene expression to modulate the immune response to the infection. However, many of these bacteria also interfere with host cellular differentiation pathways to create a hospitable niche, resulting in the formation of novel cell types, tissues, and organs. In both of these situations, bacterial symbionts must interact with eukaryotic regulatory pathways. Here, we detail what is known about how bacterial symbionts, from pathogens to mutualists, control host cellular differentiation across the central dogma, from epigenetic chromatin modifications, to transcription and mRNA processing, to translation and protein modifications. We identify four main trends from this survey. First, mechanisms for controlling host gene expression appear to evolve from symbionts co-opting cross-talk between host signalling pathways. Second, symbiont regulatory capacity is constrained by the processes that drive reductive genome evolution in host-associated bacteria. Third, the regulatory mechanisms symbionts exhibit correlate with the cost/benefit nature of the association. And, fourth symbiont mechanisms for interacting with host genetic regulatory elements are not bound by native bacterial capabilities. Using this knowledge, we explore how the ubiquitous intracellular Wolbachia symbiont of arthropods and nematodes may modulate host cellular differentiation to manipulate host reproduction. Our survey of the literature on how infection alters gene expression in Wolbachia and its hosts revealed that, despite their intermediate-sized genomes, different strains appear capable of a wide diversity of regulatory manipulations. Given this and Wolbachia’s diversity of phenotypes and eukaryotic-like proteins, we expect that many symbiont-induced host differentiation mechanisms will be discovered in this system.

Preprint ARTICLE | doi:10.20944/preprints201908.0031.v1

Aquatic Hemiptera in Southwest Cameroon: Biodiversity of Potential Reservoirs of Mycobacterium ulcerans and Multiple Wolbachia Sequence Types Revealed by Metagenomics

Seraphine N. Esemu, Xiaofeng Dong, Achah J. Kfusi, Catherine S. Hartley, Roland N. Ndip, Lucy M. Ndip, Alistair C. Darby, Rory J. Post, Benjamin L. Makepeace

Subject: Biology And Life Sciences, Insect Science Keywords: Buruli ulcer; symbiosis; Limnogonus; pond skater; riffle bug; Rhagovelia; Metrocoris; Trepobates

Online: 2 August 2019 (11:58:07 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201903.0099.v1

Gnotobiotic Rearing and Controlled Infection with Gut Symbionts Improve Adult Fitness in Transgenic Diamondback Moth, Plutella xylostella

Jasmine Somerville, Liqin Zhou, Benjamin Raymond

Subject: Biology And Life Sciences, Insect Science Keywords: genetically modified insects; symbiosis; microbiome; transgenic; self-limiting; insect rearing; mutualism

Online: 7 March 2019 (14:00:12 CET)

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Preprint ARTICLE | doi:10.20944/preprints202309.0662.v1

Dual RNA-Seq Analysis Pinpoints to a BalancedRegulation between Symbiosis and Immunity in the Medicago truncatula-Sinorhizobium meliloti Symbiotic Interactions

Dandan Zhang, Qiujin Wu, Yanwen Zhao, Ziang Yan, Aifang Xiao, Haixiang Yu, Yangrong Cao

Subject: Biology And Life Sciences, Plant Sciences Keywords: legume-rhizobial symbiosis; Medicago truncatula; Sinorhizobium meliloti; NAD1; defense; Dual RNA-seq

Online: 11 September 2023 (10:57:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.0726.v1

Promoting Sustainable Agricultural Waste Management and Industrial Symbiosis through an Innovative Web Platform

Ioannis Varvaringos, Eva Skourtanioti, Georgios Letsos, Evgenia Rizoudi, Ektoras Makras, Margarita Panagiotopoulou, Sofia Papadaki, Katerina Valta

Subject: Environmental And Earth Sciences, Sustainable Science And Technology Keywords: agricultural waste; bio-waste; synergies; web platform; bioeconomy; industrial symbiosis; waste management

Online: 21 April 2023 (13:48:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0144.v1

Genome Analysis of Two Bacterial Strains Isolated from Diseased Freshwater Sponge Reveals the Probable Cause of Its Joint Domination in Microbial Community

Ivan Petrushin, Sergei Belikov, Lubov Chernogor

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Symbiosis; Opportunistic pathogens; Janthinobacterium sp.; Flavobacterium sp.; Genomes; Floc formation; Lubomirskia baikcalensis

Online: 6 September 2020 (15:45:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.0670.v1

Arbuscular Mycorrhizal Fungi and Rhizobium Improve Nutrient Uptake and Microbial Diversity Relative to Dryland Site-Specific Soil Conditions

Rosalie Calderon, Sadikshya Dangi

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: field pea, arbuscular mycorrhizal fungi (AMF), Rhizobium, microbial inoculants, symbiosis, microbiome, agroecosystem, drylands

Online: 12 February 2024 (10:12:05 CET)

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Preprint ARTICLE | doi:10.20944/preprints202211.0472.v1

Epichloë Endophytes Shape the Foliar Endophytic Fungal Microbiome and Alter the Auxin and Salicylic Acid Phytohormone Levels in Two Meadow Fescue Cultivars

Suni Anie Mathew, Marjo Helander, Kari Saikkonen, Radomira Vankova, Petre I. Dobrev, Serdar Dirihan, Benjamin Fuchs

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: grass endophyte; Festuca; symbiosis; microbiome; plant hormone; defense response; plant-fungal interactions; holobiont

Online: 25 November 2022 (07:08:50 CET)

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Preprint ARTICLE | doi:10.20944/preprints201802.0112.v1

A Conceptual Framework for Product Service System (PSS)

Amir Pirayesh, Guy Doumeingts, Marco Seregni, Sergio Gusmeroli, Ingo Westphal, Lara Gonzalez, Carl Hans, María José Núñez Ariño, Alessandro Canepa Eugenio, Andoni Laskurain

Subject: Engineering, Industrial And Manufacturing Engineering Keywords: Product Service System (PSS); Servitization; Productization; Symbiosis; Enterprise Management; Conceptual Framework; Strategic Change

Online: 16 February 2018 (18:09:13 CET)

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Preprint REVIEW | doi:10.20944/preprints202012.0554.v1

The Microbiome and Mosquito Vectorial Capacity: Rich Potential for Discovery and Translation

Cintia Cansado-Utrilla, Serena Zhao, Philip McCall, Kerri Coon, Grant Hughes

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: microbiome; vectorial capacity; density; competence; biting; extrinsic incubation period; longevity; mosquito; symbiosis; pathogen transmission

Online: 22 December 2020 (10:49:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0305.v1

Nematode-Microbe Complexes in Soils Replanted with Apple

Xorla Kanfra, Andreas Wrede, Julia Moll, Holger Heuer

Subject: Biology And Life Sciences, Horticulture Keywords: replant disease; Malus; free-living nematodes; bacteria; fungi; rhizosphere; nematode-microbe association; disease complex; metabarcoding; nematode community

Online: 20 December 2021 (10:34:03 CET)

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Preprint REVIEW | doi:10.20944/preprints202403.1632.v1

Examining Sound, Light, and Vibrations as Tools to Manage Microbes and Support Holobionts, Ecosystems, and Technologies

Rodney R Dietert, Janice M Dietert

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: sound; acoustics, cymatics, light, quantum bacterial antennae; microbe-based technologies; energy transitions; Internet of Microbes; holobiont healing; safety

Online: 27 March 2024 (06:16:37 CET)

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Preprint REVIEW | doi:10.20944/preprints202102.0136.v1

Endophytic Fungi: Biological Control and Induced Resistance to Phytopathogens and Abiotic Stresses

Daniele Cristina Fontana, Samuel de Paula, Abel Galon Torres, Victor Hugo Moura de Souza, Sérgio Florentino Pascholati, Denise Schmidt, Durval Dourado Neto

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: endophytes; resistance inducers; biological control; abiotic stress; plant-microbe interactions; sustainability; integrated pest management; microorganisms; plant disease control

Online: 4 February 2021 (12:07:42 CET)

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Preprint ARTICLE | doi:10.20944/preprints202008.0724.v1

Gnotobiotic Evaluation of Dalbergia sissoo Genotypes for Resistance against Fusarium solani via Dual Culture Set up

Monika Chauhan, Ajay Thakur, Yashaswi Singh, M. Maqbool Rather, Nirmal S.K. Harsh

Subject: Biology And Life Sciences, Forestry Keywords: Shisham mortality; Fusarium solani f. sp. dalbergiae; in vitro screening; genetic variation; Fusarium wilt; plant-microbe interaction; gnotobiota

Online: 31 August 2020 (16:21:02 CEST)

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Preprint REVIEW | doi:10.20944/preprints202105.0131.v1

Rhizobial Exopolysaccharides: Genetic Regulation of Their Synthesis and Relevance in Symbiosis With Legumes

Sebastián Acosta-Jurado, Francisco Fuentes-Romero, Jose-Enrique Ruiz-Sainz, Monika Janczarek, José-María Vinardell

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: rhizobia; legume; rhizobium-legume symbiosis; exopolysaccharide synthesis; quorum sensing (QS); nodulation; nod regulon; flavonoids; RosR/MucR; SyrM

Online: 7 May 2021 (09:29:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201901.0058.v1

Attraction of Female Aedes aegypti (L.) to Aphid Honeydew

Daniel A.H. Peach, Regine Gries, Nathan Young, Robyn Lakes, Erin Galloway, Santosh Kumar Alamsetti, Elton Ko, Amy Ly, Gerhard Gries

Subject: Biology And Life Sciences, Insect Science Keywords: Aedes aegypti; Acyrthosiphon pisum; Myzus persicae; Vicia faba; honeydew; honeydew odorants; mosquito sugar feeding; microbe-emitted odorants; mosquito olfaction

Online: 8 January 2019 (10:13:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202210.0340.v1

Techno-economic Assessment Of An Olive Mill Wastewater (OMWW) Biorefinery In The Context Of Circular Bioeconomy

Yannis Mouzakitis, Emmanuel D. Adamides

Subject: Engineering, Industrial And Manufacturing Engineering Keywords: circular bioeconomy; biorefinery; waste valorisation; olive mill wastewater (OMWW), bioplastics; PHAs; business canvas; business model, SWOT analysis; industrial symbiosis

Online: 21 October 2022 (13:53:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201810.0640.v1

Bark Beetle Population Dynamics in the Anthropocene: Challenges and Solutions

Peter H. W. Biedermann, Jean-Claude Grégoire, Axel Gruppe, Jonas Hagge, Almuth Hammerbacher, Richard Hofstetter, Dineshkumar Kandasamy, Miroslav Kolarik, Martin Kostovcik, Paal Krokene, Jörg Müller, Aurélien Sallé, Diana L. Six, Tabea Turrini, Dan Vanderpool, Michael Wingfield, Claus Bässler

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: European spruce bark beetle, Ips, Dendroctonus, global change, symbiosis, natural enemies, population dynamics, biotic interactions, tree killing, forest pest

Online: 26 October 2018 (16:30:11 CEST)

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Preprint REVIEW | doi:10.20944/preprints202309.0482.v1

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs

Sangam L. Dwivedi, Luis Quiroz, Anireddy S.N. Reddy, Charles Spillane, Rodomiro Ortiz

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Alternative splicing; biological rhythms; domestication and polyploidization; gene mining; heterosis; nutrient homeostasis; plant phenology and architecture; symbiosis; transcriptome and proteome diversity

Online: 7 September 2023 (09:30:00 CEST)

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Working Paper HYPOTHESIS

Unveiling Human Non-random Genome Editing Mechanisms Activated in Response to Chronic Environmental Changes. I. Where Might These Mechanisms Come From?

Loris Zamai

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: environment; virus; pollutant; evolution; exaptation; stem cells; transposons; APOBEC; ADAR,; ORF2p; cancer; Eco-Evo-Devo; symbiosis; ecological genomics; environmental stress; genetic recombination; biological plasticity; hypermutation; epigenetics; fractal systems; natural selection

Online: 19 July 2020 (19:35:46 CEST)

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This article challenges the notion of the randomness of mutations in eukaryotic cells by unveiling stress-induced human non-random genome editing mechanisms. To account for the existence of such mechanisms, I have developed molecular concepts of the cell environment and cell environmental stressors and, making use of a large quantity of published data, hypothesized the origin of some crucial biological leaps along the evolutionary path of life on Earth under the pressure of natural selection, in particular, 1) virus-cell mating as a primordial form of sexual recombination and symbiosis; 2) Lamarckian CRISPR-Cas systems; 3) eukaryotic gene development; 4) antiviral activity of retrotransposon-guided mutagenic enzymes and finally; 5) the exaptation of antiviral mutagenic mechanisms to stress-induced genome editing mechanisms directed at “hypertranscribed” endogenous genes. Genes transcribed at their maximum rate (hypertranscribed), yet still unable to meet new chronic environmental demands generated by “pollution”, are inadequate and generate more and more intronic retrotransposon transcripts. In this scenario, RNA-guided mutagenic enzymes (e.g. AID/APOBECs), which have been shown to bind to retrotransposon RNA-repetitive sequences, would be surgically targeted by intronic retrotransposons on opened chromatin regions of the same “hypertranscribed” genes. RNA-guided mutagenic enzymes may therefore “Lamarkianly” generate single nucleotide polymorphisms (SNP) and copy number variations (CNV), as well as transposon transposition and chromosomal translocations in the restricted areas of hyperfunctional and inadequate genes, leaving intact the rest of the genome. CNV and SNP of hypertranscribed genes may allow cells to surgically explore a new fitness scenario, which increases their adaptability to stressful environmental conditions. Like the mechanisms of immunoglobulin somatic hypermutation, non-random genome editing mechanisms may generate several cell mutants, and those codifying for the most environmentally-adequate proteins would have a survival advantage and would therefore be Darwinianly selected. Non-random genome editing mechanisms represent a link between environmental changes and biological novelty and plasticity, and provide a molecular basis to reconcile gene-centered and “ecological” views of evolution.

Preprint ARTICLE | doi:10.20944/preprints202308.1417.v1

Impacts of Natural Selection on Evolution of Core and Symbiotically Specialized Genes in the Polytypic Species Neorhizobium galegae

Evgeny S. Karasev, Hosid L. Sergey, Tatiana S. Aksenova, Olga P. Onishchuk, Oksana N. Kurchak, Nikolay I. Dzyubenko, Evgeny E. Andronov, Nikolay A. Provorov

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Neorhizobium galegae biovars orientalis and officinalis; polytypic rhizobia species; evolution of symbiosis; core and symbiotically specialized (sym) genes; nucleotide polymorphism of genes; driving and purifying selection; p-distance; dN/dS statistics; goats’ rue (Galega); Illumina

Online: 21 August 2023 (07:26:27 CEST)

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Nodule bacteria (rhizobia) represent a suitable model to address a range of evolutionary prob-lems including the tradeoff between genetic polymorphism and natural selection. Rhizobia possess the complicated genomes in which symbiotically specialized (sym) genes differ in their natural histories from core genes encoding for housekeeping functions. Diversification of sym genes is responsible for the rhizobia microevolution which depends on the host-induced natural selection. For the rhizobia speciation, diversification of core genes is responsible for which the selective factors are unclear. In this paper we demonstrate that in the goats’ rue rhizobia (Neorhizobium galegae) populations collected at North Caucasus and composed of two host-specific biovars orientalis and officianalis (N2-fixing symbionts of Galega orientalis and G. officinalis, respectively), evolutionary mechanisms are different for core and sym genes. In both N. galegae biovars, core genes are more polymorphic than sym genes. In bv. orientalis, evolution of core genes occurs under the impacts of driving se-lection (dN/dS > 1), while evolution of sym genes is close to neutral (dN/dS ≈ 1). In bv. officinalis, evolution of core genes is neutral, while for sym genes, it is dependent on purifying selection (dN/dS < 1). A marked phylogenetic congruence of core and sym genes revealed using the ANI analysis may be due to a low intensity of gene transfer within and between N. galegae biovars. Polymorphism of both gene groups and the impacts of driving selection on the core gene evolu-tion are more pronounced in bv. orientalis than in bv. officianalis reflecting the diversities of re-spective host plant species. In bv. orientalis, highly significant (P0 < 0,001) positive correlation was revealed between the p-distance and dN/dS values for core genes, while in bv. officinalis this cor-relation is lowly significant (0,05 < P0 < 0,10). For sym genes, correlation between the p-distance and dN/dS values is negative in bv. officinalis but is not revealed in bv. orientalis. These data along with the functional annotation of core genes implemented using the Gene Ontology tools sug-gests that evolution of bv. officinalis is based mostly on adaptation for in planta niches while in bv. orientalis evolution presumable depends on adaptation for soil niches. New insights into the tradeoff between natural selection and genetic diversity are presented suggesting that the gene polymorphism may be extended by driving selection only in the ecologically versatile organ-isms capable to support a broad spectrum of gene alleles in their genepools.

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