Works in Environmental Microbiome, 2024, Vol 19, Issue 1

Results: 108

Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00576-3

By:

Benalcazar, Paul;
Seuradge, Brent;
Diochon, Amanda C.;
Kolka, Randall K.;
Phillips, Lori A.

Publication type:

Article

Integrating depth-dependent protist dynamics and microbial interactions in spring succession of a freshwater reservoir.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00574-5

By:

Mukherjee, Indranil;
Grujčić, Vesna;
Salcher, Michaela M.;
Znachor, Petr;
Seďa, Jaromír;
Devetter, Miloslav;
Rychtecký, Pavel;
Šimek, Karel;
Shabarova, Tanja

Publication type:

Article

Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00571-8

By:

Erlandson, Sonya R.;
Ewing, Patrick M.;
Osborne, Shannon L.;
Lehman, R. Michael

Publication type:

Article

Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00572-7

By:

Liew, Kok Jun;
Shahar, Saleha;
Shamsir, Mohd Shahir;
Shaharuddin, Nawal Binti;
Liang, Chee Hung;
Chan, Kok-Gan;
Pointing, Stephen Brian;
Sani, Rajesh Kumar;
Goh, Kian Mau

Publication type:

Article

Ecology of aerobic anoxygenic phototrophs on a fine-scale taxonomic resolution in Adriatic Sea unravelled by unsupervised neural network.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00573-6

By:

Stojan, Iva;
Šantić, Danijela;
Villena-Alemany, Cristian;
Trumbić, Željka;
Matić, Frano;
Vrdoljak Tomaš, Ana;
Lepen Pleić, Ivana;
Piwosz, Kasia;
Kušpilić, Grozdan;
Ninčević Gladan, Živana;
Šestanović, Stefanija;
Šolić, Mladen

Publication type:

Article

Microbial communities colonising plastics during transition from the wastewater treatment plant to marine waters.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00569-2

By:

Tulloch, Constance L.;
Bargiela, Rafael;
Williams, Gwion B.;
Chernikova, Tatyana N.;
Cotterell, Benjamin M.;
Wellington, Elizabeth M. H.;
Christie-Oleza, Joseph;
Thomas, David N.;
Jones, Davey L.;
Golyshin, Peter N.

Publication type:

Article

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00570-9

By:

Goff, Jennifer L.;
Szink, Elizabeth G.;
Durrence, Konnor L.;
Lui, Lauren M.;
Nielsen, Torben N.;
Kuehl, Jennifer V.;
Hunt, Kristopher A.;
Chandonia, John-Marc;
Huang, Jiawen;
Thorgersen, Michael P.;
Poole II, Farris L.;
Stahl, David A.;
Chakraborty, Romy;
Deutschbauer, Adam M.;
Arkin, Adam P.;
Adams, Michael W. W.

Publication type:

Article

The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00562-9

By:

Ghezzi, Daniele;
Jiménez-Morillo, Nicasio Tomás;
Foschi, Lisa;
Donini, Eva;
Chiarini, Veronica;
De Waele, Jo;
Miller, Ana Zélia;
Cappelletti, Martina

Publication type:

Article

Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00566-5

By:

Lailheugue, Vincent;
Darriaut, Romain;
Tran, Joseph;
Morel, Marine;
Marguerit, Elisa;
Lauvergeat, Virginie

Publication type:

Article

Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00568-3

By:

Wainwright, Benjamin J.;
Leon, Josh;
Vilela, Ernie;
Hickman, K. J. E.;
Caldwell, Jensen;
Aimone, Behlee;
Bischoff, Porter;
Ohran, Marissa;
Morelli, Magnolia W.;
Arlyza, Irma S.;
Marwayana, Onny N.;
Zahn, Geoffrey

Publication type:

Article

Niche–dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00563-8

By:

Liu, Fang;
Ryu, Taewoo;
Ravasi, Timothy;
Wang, Xin;
Wang, Guangyi;
Li, Zhiyong

Publication type:

Article

City-scale monitoring of antibiotic resistance genes by digital PCR and metagenomics.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00557-6

By:

Maestre-Carballa, Lucia;
Navarro-López, Vicente;
Martinez-Garcia, Manuel

Publication type:

Article

Fungal and bacterial communities and their associations in snow-free and snow covered (sub-)alpine Pinus cembra forest soils.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00564-7

By:

Probst, Maraike;
Telagathoti, Anusha;
Mandolini, Edoardo;
Peintner, Ursula

Publication type:

Article

An in-depth evaluation of metagenomic classifiers for soil microbiomes.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00561-w

By:

Edwin, Niranjana Rose;
Fitzpatrick, Amy Heather;
Brennan, Fiona;
Abram, Florence;
O'Sullivan, Orla

Publication type:

Article

Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00559-4

By:

Romdhane, Sana;
Huet, Sarah;
Spor, Aymé;
Bru, David;
Breuil, Marie-Christine;
Philippot, Laurent

Publication type:

Article

Pitting the olive seed microbiome.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00560-x

By:

Wentzien, Nuria M.;
Fernández-González, Antonio J.;
Valverde-Corredor, Antonio;
Lasa, Ana V.;
Villadas, Pablo J.;
Wicaksono, Wisnu Adi;
Cernava, Tomislav;
Berg, Gabriele;
Fernández-López, Manuel;
Mercado-Blanco, Jesús

Publication type:

Article

Forest top canopy bacterial communities are influenced by elevation and host tree traits.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00565-6

By:

Duan, Yiwei;
Siegenthaler, Andjin;
Skidmore, Andrew K.;
Chariton, Anthony A.;
Laros, Ivo;
Rousseau, Mélody;
De Groot, G. Arjen

Publication type:

Article

Microbiome changes through the ontogeny of the marine sponge Crambe crambe.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00556-7

By:

Turon, Marta;
Ford, Madeline;
Maldonado, Manuel;
Sitjà, Cèlia;
Riesgo, Ana;
Díez-Vives, Cristina

Publication type:

Article

Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00558-5

By:

Thomas, Vanessa E.;
Antony-Babu, Sanjay

Publication type:

Article

Niche differentiation and biogeography of Bathyarchaeia in paddy soil ecosystems: a case study in eastern China.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00555-8

By:

Yi, Xingyun;
Brandt, Kristian Koefoed;
Xue, Shudan;
Peng, Jingjing;
Wang, Yifei;
Li, Meng;
Deng, Ye;
Duan, Guilan

Publication type:

Article

Bacterial wilt affects the structure and assembly of microbial communities along the soil-root continuum.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00548-7

By:

Liang, Jinchang;
Wei, Chengjian;
Song, Xueru;
Wang, Rui;
Shi, Heli;
Tan, Jun;
Cheng, Dejie;
Wang, Wenjing;
Wang, Xiaoqiang

Publication type:

Article

Plant effects on microbiome composition are constrained by environmental conditions in a successional grassland.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00550-z

By:

Mészárošová, Lenka;
Kuťáková, Eliška;
Kohout, Petr;
Münzbergová, Zuzana;
Baldrian, Petr

Publication type:

Article

Weather in two climatic regions shapes the diversity and drives the structure of fungal endophytic community of bilberry (Vaccinium myrtillus L.) fruit.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00551-y

By:

Nguyen, Minh-Phuong;
Lehosmaa, Kaisa;
Toth, Katalin;
Koskimäki, Janne J.;
Häggman, Hely;
Pirttilä, Anna Maria

Publication type:

Article

The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00552-x

By:

de Souza, Yuri Pinheiro Alves;
Schloter, Michael;
Weisser, Wolfgang;
Huang, Yuanyuan;
Schulz, Stefanie

Publication type:

Article

Identification of potential microbial risk factors associated with fecal indicator exceedances at recreational beaches.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00547-8

By:

Saleem, Faizan;
Li, Enze;
Edge, Thomas A.;
Tran, Kevin L.;
Schellhorn, Herb E.

Publication type:

Article

Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-023-00546-1

By:

Wang, Wenqian;
Li, Dongmei;
Qiu, Xiaoqian;
Yang, Jinshui;
Liu, Liang;
Wang, Entao;
Yuan, Hongli

Publication type:

Article

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-023-00545-2

By:

Centurion, Victor Borin;
Rossi, Alessandro;
Orellana, Esteban;
Ghiotto, Gabriele;
Kakuk, Balázs;
Morlino, Maria Silvia;
Basile, Arianna;
Zampieri, Guido;
Treu, Laura;
Campanaro, Stefano

Publication type:

Article

The road forward to incorporate seawater microbes in predictive reef monitoring.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-023-00543-4

By:

Terzin, Marko;
Laffy, Patrick W.;
Robbins, Steven;
Yeoh, Yun Kit;
Frade, Pedro R.;
Glasl, Bettina;
Webster, Nicole S.;
Bourne, David G.

Publication type:

Article

Phytoplankton ecology in the early years of a boreal oil sands end pit lake.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-023-00544-3

By:

Furgason, Chantel C.;
Smirnova, Angela V.;
Dacks, Joel B.;
Dunfield, Peter F.

Publication type:

Article

Microbial diversity and biogeochemical interactions in the seismically active and CO<sub>2</sub>- rich Eger Rift ecosystem.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00651-9

By:

Lipus, Daniel;
Jia, Zeyu;
Sondermann, Megan;
Bussert, Robert;
Bartholomäus, Alexander;
Yang, Sizhong;
Wagner, Dirk;
Kallmeyer, Jens

Publication type:

Article

High diversity of crustose coralline algae microbiomes across species and islands, and implications for coral recruits.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00640-y

By:

Hochart, Corentin;
Rouzé, Héloïse;
Rivière, Béatrice;
Ruscheweyh, Hans-Joachim;
Hédouin, Laetitia;
Pochon, Xavier;
Steneck, Robert S.;
Poulain, Julie;
Belser, Caroline;
Nugues, Maggy M.;
Galand, Pierre E.

Publication type:

Article

The microorganisms and metabolome of Pinus radiata Pollen.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00656-4

By:

Armstrong, Charlotte;
Ganasamurthy, Syaliny;
Wigley, Kathryn;
Mercier, Celine;
Wakelin, Steve

Publication type:

Article

Nutritional niches of potentially endemic, facultatively anaerobic heterotrophs from an isolated Antarctic terrestrial hydrothermal refugium elucidated through metagenomics.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00655-5

By:

Herbold, Craig W.;
Noell, Stephen E.;
Lee, Charles K.;
Vickers, Chelsea J.;
Stott, Matthew B.;
Eisen, Jonathan A.;
McDonald, Ian R.;
Cary, S. Craig

Publication type:

Article

Herbicide-treated soil as a reservoir of beneficial bacteria: microbiome analysis and PGP bioinoculants in maize.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00654-6

By:

Galic, Ivana;
Bez, Cristina;
Bertani, Iris;
Venturi, Vittorio;
Stankovic, Nada

Publication type:

Article

Effects of pepper–maize intercropping on the physicochemical properties, microbial communities, and metabolites of rhizosphere and bulk soils.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00653-7

By:

Chen, Zeli;
Wang, Wenzhi;
Chen, Lu;
Zhang, Peng;
Liu, Zhenhuan;
Yang, Xukun;
Shao, Jinliang;
Ding, Yan;
Mi, Yanhua

Publication type:

Article

Microbiome associated to an H<sub>2</sub>-emitting zone in the São Francisco basin Brazil.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00627-9

By:

Pinto, Otávio Henrique Bezerra;
Oliveira, Rafael da Silva;
Ferreira, Brendo Ramos;
Peixoto, Julianna;
Sartori, Maria Regina Silveira;
Quirino, Betania Ferraz;
Brunet, Fabrice;
Kruger, Ricardo Henrique

Publication type:

Article

Unveiling the bacterial diversity and potential of the Avicennia marina ecosystem for enhancing plant resilience to saline conditions.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00642-w

By:

Alghamdi, Amal Khalaf;
Parween, Sabiha;
Hirt, Heribert;
Saad, Maged M.

Publication type:

Article

Stochasticity-dominated rare fungal endophytes contribute to coexistence stability and saponin accumulation in Panax species.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00645-7

By:

Liu, Ye;
Shi, Liping;
Hong, Fei;
Wei, Guangfei;
Jiang, Zhenzhen;
Wei, Xiuye;
Peng, Jingjing;
Zhang, Guozhuang;
Dong, Linlin

Publication type:

Article

Shear stress controls prokaryotic and eukaryotic biofilm communities together with EPS and metabolomic expression in a semi-controlled coastal environment in the NW Mediterranean Sea.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00647-5

By:

Portas, Aurélie;
Carriot, Nathan;
Barry-Martinet, Raphaëlle;
Ortalo-Magné, Annick;
Hajjoul, Houssam;
Dormoy, Bruno;
Culioli, Gérald;
Quillien, Nolwenn;
Briand, Jean-François.

Publication type:

Article

Arctic's hidden hydrocarbon degradation microbes: investigating the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on microbial communities and hydrocarbon biodegradation pathways in high-Arctic beaches.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00626-w

By:

Chen, Ya-Jou;
Altshuler, Ianina;
Freyria, Nastasia J.;
Lirette, Antoine;
Góngora, Esteban;
Greer, Charles W.;
Whyte, Lyle G.

Publication type:

Article

Millennial-scale microbiome analysis reveals ancient antimicrobial resistance conserved despite modern selection pressures.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00652-8

By:

Gomathinayagam, Sankaranarayanan;
Kanagalingam, Swathi;
Chandrasekaran, Srimathi;
Krishnan, Thirumoorthy;
Kodiveri Muthukaliannan, Gothandam

Publication type:

Article

1,2-DCA biodegradation potential of an aquifer assessed in situ and in aerobic and anaerobic microcosms.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00650-w

By:

Cruciata, Ilenia;
Scirè Calabrisotto, Laura;
Carpani, Giovanna;
Poppa, Lucia;
Modica, Alfonso;
Pace, Andrea;
Catania, Valentina;
Quatrini, Paola

Publication type:

Article

Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00649-3

By:

Amano, Yuki;
Sachdeva, Rohan;
Gittins, Daniel;
Anantharaman, Karthik;
Lei, Shufei;
Valentin-Alvarado, Luis E.;
Diamond, Spencer;
Beppu, Hikari;
Iwatsuki, Teruki;
Mochizuki, Akihito;
Miyakawa, Kazuya;
Ishii, Eiichi;
Murakami, Hiroaki;
Jaffe, Alexander L.;
Castelle, Cindy;
Lavy, Adi;
Suzuki, Yohey;
Banfield, Jillian F.

Publication type:

Article

Regional scale diversity and distribution of soil inhabiting Tetracladium.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00646-6

By:

Lazar, Anna;
Griffiths, Robert I.;
Goodall, Tim;
Norton, Lisa R.;
Mushinski, Ryan M.;
Bending, Gary D.

Publication type:

Article

Impact of foliar application of phyllosphere yeast strains combined with soil fertilizer application on rice growth and yield.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00635-9

By:

Muthukrishanan, Gomathy;
Munisamy, Jeyashri;
Gopalasubramaniam, Sabarinathan Kuttalingam;
Subramanian, Kizaharael Sevathapandian;
Dharmaraj, Rajakumar;
Nath, Dhruba Jyoti;
Dutta, Pranab;
Devarajan, Arun Kumar

Publication type:

Article

Evidence of habitat specificity in sponge microbiomes from Antarctica.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00648-4

By:

Manrique-de-la-Cuba, Maria F.;
Parada-Pozo, Génesis;
Rodríguez-Marconi, Susana;
López-Rodríguez, Marileyxis R.;
Abades, Sebastián;
Trefault, Nicole

Publication type:

Article

Alpine and subalpine plant microbiome mediated plants adapt to the cold environment: A systematic review.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00614-0

By:

Hou, Mengyan;
Leng, Chunyan;
Zhu, Jun;
Yang, Mingshu;
Yin, Yifei;
Xing, Yongmei;
Chen, Juan

Publication type:

Article

Selenium alters the gene content but not the taxonomic composition of the soil microbiome.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00641-x

By:

Bennett, Alison E.;
Kelsey, Scott;
Saup, Casey;
Wilkins, Mike;
Malacrinò, Antonino

Publication type:

Article

Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00639-5

By:

Richy, Etienne;
Thiago Dobbler, Priscila;
Tláskal, Vojtěch;
López-Mondéjar, Rubén;
Baldrian, Petr;
Kyselková, Martina

Publication type:

Article

Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.

Published in:

Environmental Microbiome, 2024, v. 19, n. 1, p. 1, doi. 10.1186/s40793-024-00632-y

By:

Paquette, Alexandre J.;
Bhatnagar, Srijak;
Vadlamani, Agasteswar;
Gillis, Timber;
Khot, Varada;
Novotnik, Breda;
De la Hoz Siegler, Hector;
Strous, Marc;
Rattray, Jayne E.

Publication type:

Article