Article
Biology
Afef Najjari, Panagiota Stathopoulou, Khaled Elmnasri, Faten Hasnaoui, Ines Zidi, Haitham Sghaier, Hadda Imene Ouzari, Ameur Cherif, George Tsiamis
Summary: This study comprehensively evaluated the archaeal diversity in three different halite-crystal salts from two separate saline systems in Southern Tunisia, revealing unexpected diversity profiles and demonstrating that the Miseq approach can detect more diversity compared to other methods.
Article
Ecology
Zivile Buivydaite, Mille Anna Lilja, Rumakanta Sapkota, Benni Winding Hansen, Lea Ellegaard-Jensen, Niels Bohse Hendriksen, Paul Henning Krogh, Anne Winding
Summary: Earthworms play an important role in soil ecosystem functioning and are used as indicators of ecosystem health. This study investigates the interactions between earthworms and soil microorganisms by comparing soil with and without earthworms in microcosms. The results show that earthworms increase microbial activity, decrease species richness, and shape soil prokaryotes community structure. Certain bacterial phyla were enriched, while the relative abundance of the archaeal phylum Thaumarchaeota decreased in the presence of earthworms. The study highlights the influence of earthworms on soil microbial communities and their activity, suggesting the need to incorporate earthworm-prokaryote interactions in future soil microbiome studies.
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2023)
Article
Microbiology
Alba Regueira-Iglesias, Lara Vazquez-Gonzalez, Carlos Balsa-Castro, Nicolas Vila-Blanco, Triana Blanco-Pintos, Javier Tamames, Maria Jose Carreira, Inmaculada Tomas
Summary: This study analyzed the coverage of 16S rRNA gene primers used in oral microbiome studies and identified the best primers. The findings showed that the optimal primers can be utilized for detecting both oral bacteria and archaea, with a wide coverage range.
Article
Environmental Sciences
Celine Lavergne, Polette Aguilar-Munoz, Natalia Calle, Frederic Thalasso, Maria Soledad Astorga-Espana, Armando Sepulveda-Jauregui, Karla Martinez-Cruz, Laure Gandois, Andres Mansilla, Rolando Chamy, Maialen Barret, Lea Cabrol
Summary: Freshwater ecosystems play a significant role in methane emissions and this study investigated the effects of temperature on microbial community structure and methane production pathways in sub-Antarctic lake sediments. The research found that temperature had a significant impact on methane production rates, particularly when methanogenic precursors such as acetate and H-2/CO2 were introduced.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Environmental Sciences
Blaire M. Padayhag, Michael Angelou L. Nada, Jake Ivan P. Baquiran, Marilou P. Sison-Mangus, Maria Lourdes San Diego-McGlone, Patrick C. Cabaitan, Cecilia Conaco
Summary: This study found that the microbial biofilm communities near mariculture areas can affect the settlement of coral larvae. The biofilm farthest from the mariculture area had a higher effectiveness in inducing the settlement of Acropora tenuis larvae. These biofilms were characterized by a greater proportion of crustose coralline algae and gammaproteobacterial taxa, while biofilms closer to the mariculture zone had a higher proportion of cyanobacteria and no crustose coralline algae. These findings suggest that nutrient enrichment from mariculture activities can alter the composition of biofilm-associated microbiome and indirectly affect coral larval settlement.
MARINE POLLUTION BULLETIN
(2023)
Article
Biochemistry & Molecular Biology
Magdalena Nagler, Sabine Marie Podmirseg, Markus Mayr, Judith Ascher-Jenull, Heribert Insam
Summary: Microbiome studies using next generation sequencing are commonly performed on the total DNA pool, which includes extracellular- and intracellular DNA fractions. Results show that total DNA has lower species richness and unique reads compared to intracellular DNA when tracking microbial community changes over time. The extracellular DNA fraction may qualitatively bias microbiome studies due to abundant sequences masking overall results, while intracellular DNA provides more reliable genetic information about potentially alive microbes.
Article
Environmental Sciences
Olivier Laroche, Sonnich Meier, Svein A. Mjos, Nigel Keeley
Summary: This study examined the impact of salmon farming on several epibenthic suspension-feeders and identified potential molecular indicators of this impact. The results showed species-specific effects and differences in fatty acid profiles and host microbiome communities.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Multidisciplinary Sciences
Valsamma Joseph, Geethu Chellappan, S. Aparajitha, R. N. Ramya, S. Vrinda, V. J. Rejish Kumar, I. S. Bright Singh
Summary: The study on bacterial and archaeal communities in a zero-water exchange shrimp culture pond maintained with indigenous bioaugmentor revealed their significant roles in cycling carbon, nitrogen, and sulphur, leading to efficient bioremediation. Gene-specific analysis highlighted the importance of specific ammonia-oxidizing bacteria and archaea in removing accumulated ammonia, maintaining healthy environmental conditions in the pond.
SN APPLIED SCIENCES
(2021)
Article
Microbiology
Haitao Wang, Alexandre Bagnoud, Rafael Ponce-Toledo, Melina Kerou, Micha Weil, Christa Schleper, Tim Urich
Summary: The newly established taxonomy for AOA based on amoA provides a finer resolution and reveals novel environmental patterns. By linking 16S rRNA gene classification to this novel taxonomy through phylogenetic congruence, it allows for the identification of specific AOA clades. This approach provides a pathway for interpreting the ecology of globally abundant AOA, especially when using 16S rRNA gene sequencing data in microbiome studies.
Article
Environmental Sciences
Ademir Sergio Ferreira Araujo, Ana Roberta Lima Miranda, Arthur Prudencio de Araujo Pereira, Wanderley Jose de Melo, Vania Maria Maciel Melo, Sabrina Hermelindo Ventura, Eudemio Sousa Brito Jr, Erika Valente de Medeiros, Fabio Fernando Araujo, Lucas William Mendes
Summary: This study assessed the microbial community in the rhizosphere of maize and cowpea grown in Cr-contaminated soils using amplicon sequencing. The results showed that the microbial community in the maize rhizosphere clustered together, while the microbial community in the cowpea rhizosphere did not present clear clustering. Furthermore, Cr contamination had different effects on specific bacterial groups in the rhizospheres of maize and cowpea.
Article
Microbiology
Jiun-Nong Lin, Chung-Hsu Lai, Shang-Yi Lin, Ching-Chi Lee, Nan-Yao Lee, Po-Yu Liu, Chih-Hui Yang, Yi-Han Huang
Summary: This study evaluated the impact of intraspecific diversity among the multiple copies of the 16S rRNA gene on the accuracy of species identification in the genus Elizabethkingia. The results suggest that 16S rRNA gene sequencing should not be considered the gold standard for the accurate identification of Elizabethkingia species.
MICROBIOLOGY SPECTRUM
(2022)
Article
Agronomy
Santosh Ranjan Mohanty, Manoj Parihar, Garima Dubey, Rakesh Parmar, Devendra Jain, Muneshwar Singh, Ashok Patra, Suresh Kumar Chaudhari, Bharati Kollah
Summary: This study estimates nitrification and elucidates the mechanistic processes of nitrogen mineralization in a long-term fertilizer experiment on a soybean-wheat cropping system. The results show that continuous cropping without fertilizer can alter soil microbial metabolism for the acquisition of nitrogen from mineralization of readily unavailable mineral fractions.
ARCHIVES OF AGRONOMY AND SOIL SCIENCE
(2022)
Article
Green & Sustainable Science & Technology
Eka Sunarwidhi Prasedya, Nanda Sofian Hadi Kurniawan, Fitriani Fitriani, Putu Bella Aprillia Saraswati, Wanda Qoriasmadillah, Bq Tri Khairina Ilhami, Ari Hernawan, Sri Widyastuti
Summary: The frequent use of chemical fertilizers in agriculture has become an urgent environmental concern. This study investigates the potential of seaweed fertilizer as an alternative to chemical fertilizers. The findings show that seaweed fertilizer enhances plant growth and soil beneficial microbiota, increases the availability of macronutrients in the soil, and enriches functional genes and proteins related to metabolism. These findings improve our understanding of the importance of microbial community for soil quality and demonstrate the positive impact of seaweed supplementation on soil fertility and rice plant growth.
Article
Biophysics
Tomoyuki Taguchi, Machi Ishikawa, Momoko Ichikawa, Takashi Tadenuma, Yuko Hirakawa, Tomoko Yoshino, Yoshiaki Maeda, Hiyori Takeuchi, Daisuke Nojima, Takeo Tanaami, Tadashi Matsunaga, Tsuyoshi Tanaka
Summary: In this study, a novel DNA microarray system was developed that eliminates the need for labeling, amplification, or washing of target nucleic acid fragments. By using specially designed DNA probes, the system allows for quick and specific detection of DNA and RNA within a short period of time.
BIOSENSORS & BIOELECTRONICS
(2021)
Review
Microbiology
Guillaume Tahon, Patricia Geesink, Thijs J. G. Ettema
Summary: The discovery and study of Archaea in the past few decades have greatly expanded our understanding of their cell biology, physiology, ecology, and diversity. However, due to computational limitations and the ongoing discovery of new lineages, a stable archaeal phylogeny has not yet been achieved. Therefore, obtaining consensus on the phylogenetic and taxonomic classification of Archaea should be a high priority for the research community.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021
(2021)