New globally distributed bacterial phyla within the FCB superphylum DOI Creative Commons
Xianzhe Gong, Álvaro Rodríguez del Río, Xu Le

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Dec. 6, 2022

Abstract Microbes in marine sediments play crucial roles global carbon and nutrient cycling. However, our understanding of microbial diversity physiology on the ocean floor is limited. Here, we use phylogenomic analyses thousands metagenome-assembled genomes (MAGs) from coastal deep-sea to identify 55 MAGs that are phylogenetically distinct previously described bacterial phyla. We propose these belong 4 novel phyla (Blakebacterota, Orphanbacterota, Arandabacterota, Joyebacterota) a proposed phylum (AABM5-125-24), all them within FCB superphylum. Comparison their rRNA genes with public databases reveals globally distributed different habitats, including marine, freshwater, terrestrial environments. Genomic suggest organisms capable mediating key steps sedimentary biogeochemistry, anaerobic degradation polysaccharides proteins, respiration sulfur nitrogen. Interestingly, code for an unusually high proportion (~9% average, up 20% per genome) protein families lacking representatives databases. Genes encoding hundreds colocalize predicted be involved reduction, nitrogen cycling, energy conservation, organic compounds. Our findings advance diversity, ecological bacteria, potential links between gene metabolic processes oceans.

Language: Английский

Mapping the soil microbiome functions shaping wetland methane emissions DOI Open Access
Angela Oliverio, Adrienne B. Narrowe, Jorge A. Villa

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 7, 2024

Accounting for only 8% of Earth's land coverage, freshwater wetlands remain the foremost contributor to global methane emissions. Yet microorganisms and processes underlying emissions from wetland soils poorly understood. Over a five-year period, we surveyed microbial membership in situ measurements over 700 samples one most prolific methane-emitting United States. We constructed catalog 2,502 metagenome-assembled genomes (MAGs), with nearly half 72 bacterial archaeal phyla sampled containing novel lineages. Integration these data 133 soil metatranscriptomes provided genome-resolved view biogeochemical specialization versatility expressed soils. Centimeter-scale depth differences best explained patterns community structure transcribed functionalities, even more so than coverage or temporal information. Moreover, while extended flooding restructured redox, this perturbation failed reconfigure transcriptional profiles cycling microorganisms, contrasting theoretical expected responses hydrological perturbations. Co-expression analyses coupled resolved exposed metabolisms trophic structures predictive hotspots. This compendium biogeochemically-classified their spatiotemporal begins untangle carbon, energy nutrient processing contributing production.

Language: Английский

Citations

5
Rare subcommunity maintains the stability of ecosystem multifunctionality by deterministic assembly processes in subtropical estuaries DOI Creative Commons
Yang Shu, Qinghua Hou, Nan Li

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: April 19, 2024

Microorganisms, especially rare microbial species, are crucial in estuarine ecosystems for driving biogeochemical processes and preserving biodiversity. However, the understanding of links between ecosystem multifunctionality (EMF) diversity bacterial taxa estuary remains limited. Employing high-throughput sequencing a variety statistical methods, we assessed diversities assembly process abundant bacterioplankton their contributions to EMF subtropical estuary. Taxonomic analysis revealed Proteobacteria as predominant phylum among both taxa. Notably, demonstrated significantly higher taxonomic larger species pool than Additionally, our findings highlighted that deterministic predominantly shape communities, with heterogeneous selection exerting stronger influence on Further reveals beta-diversity impacts EMF, whereas alpha did not. The partial least squares path modeling (PLS-PM) beta taxa, main biotic factor, directly affected while temperature total organic carbon (TOC) were additional key factors determine relationship EMF. These advance distribution features ecological knowledge estuaries, provide reference exploring different biospheres aquatic environments.

Language: Английский

Citations

5
Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments DOI
Xianzhe Gong, Zhiyi Chen,

Ye Deng

et al.

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 852, P. 158411 - 158411

Published: Aug. 31, 2022

Language: Английский

Citations

21
Understanding Interaction Patterns within Deep-Sea Microbial Communities and Their Potential Applications DOI Creative Commons
Muhammad Zohaib Nawaz, Raghul Subin Sasidharan, Ahmed Al‐Emam

et al.

Marine Drugs, Journal Year: 2022, Volume and Issue: 20(2), P. 108 - 108

Published: Jan. 28, 2022

Environmental microbes living in communities engage complex interspecies interactions that are challenging to decipher. Nevertheless, the provide basis for shaping community structure and functioning, which is crucial ecosystem service. In addition, microbial facilitate specific adaptation ecological evolution processes particularly essential dwelling resource-limiting habitats, such as deep oceans. Recent technological knowledge advancements an opportunity study of within communities, those inhabiting deep-sea waters sediments. The interaction studies insights into developing new strategies biotechnical applications. For example, cooperative drive degradation organic matter chitins celluloses. Such microbiologically-driven biogeochemical stimulate creative designs many applied sciences. Understanding mechanisms provides development synthetic consequently achievement functions. Microbial engineering has application potentials, including production novel antibiotics, biofuels, other valuable chemicals biomaterials. It can also be developed biotechniques waste processing environmental contaminant bioremediation. This review summarizes our current understanding emerging techniques inferring aiding future biotechnological therapeutic

Language: Английский

Citations

20
Catabolic protein degradation in marine sediments confined to distinct archaea DOI Creative Commons
Xiuran Yin, Guo‐Wei Zhou, Mingwei Cai

et al.

The ISME Journal, Journal Year: 2022, Volume and Issue: 16(6), P. 1617 - 1626

Published: Feb. 26, 2022

Abstract Metagenomic analysis has facilitated prediction of a variety carbon utilization potentials by uncultivated archaea including degradation protein, which is wide-spread polymer in marine sediments. However, the activity detrital catabolic protein mostly unknown for vast majority archaea. Here, we show actively executed catabolism three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota 2c) RNA- and lipid-stable isotope probing incubations with different highly abundant potential degraders Thermoprofundales (MBG-D) 3 were not incorporating 13C-label from during incubations. Nonetheless, found that pathway was present metagenome associated genomes (MAGs) active inactive This finding supported screening extracellular peptidases 180 MAGs, appeared to be widespread but correlated organisms executing this process our Thus, results have important implications: (i) multiple low-abundant groups are actually degraders; (ii) functional role an optimal tool identify catabolism, (iii) sedimentary common feature community temperate permanently cold

Language: Английский

Citations

20
Recycling eutrophic lake sediments into grass production: A four-year field experiment on agronomical and environmental implications DOI Creative Commons
Mina Kiani, Jure Zrim, Asko Simojoki

et al.

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 870, P. 161881 - 161881

Published: Jan. 30, 2023

Inefficient use of phosphorus (P) fertilizers leads to the transfer P into water bodies, causing their eutrophication. Sediment removal is a promising lake restoration strategy that removes nutrients including accumulated in sediments, and opens opportunity removed agriculture. In present study, we investigated effects using thick layer sediment from eutrophic Lake Mustijärv on plant growth, estimated environmental impacts different application methods by analyzing greenhouse gas emissions, N leaching, aggregate stability, soil biota. The field experiment (2017-2020) was established shore with following treatments: agricultural control (Soil) surrounding lake, pure (Sed), biochar-treated (SB), biochar mixed (SSB). sediment-based treatments resulted similar grass growth performance Soil. availability most macro- micronutrients (75 vs. 21 g m-3) were far greater Sed compared growing media emitted more CO2 than Soil (579 400 mg - C m-2 h-1) presumably due high rate organic matter decomposition. bacterial fungal community structures strongly differentiated those Also, had lower diversity higher abundance phyla associated solubilizing Proteobacteria Chloroflexi. Sediment-based increased seven times risk mineral treatment only short-lived beneficial effect reduction sediment's leached concentration. should be adjusted match crop requirements minimize emissions nutrient leaching when upscaling case study larger lakes properties.

Language: Английский

Citations

13
Contrasting benthic bacterial and fungal communities in two temperate coastal areas affected by different levels of anthropogenic pressure DOI
Zhen Wang, Xiaohan Liu, Xiaocheng Wang

et al.

Marine Environmental Research, Journal Year: 2024, Volume and Issue: 198, P. 106501 - 106501

Published: April 9, 2024

Language: Английский

Citations

4
Metagenomics study in aquatic resource management: Recent trends, applied methodologies and future needs DOI
Bijay Kumar Behera, Budheswar Dehury, Ajaya Kumar Rout

et al.

Gene Reports, Journal Year: 2021, Volume and Issue: 25, P. 101372 - 101372

Published: Oct. 1, 2021

Language: Английский

Citations

25
Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface DOI Creative Commons
Paraskevi Mara, David Geller-McGrath, Virginia P. Edgcomb

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 27, 2023

Abstract Previous studies of microbial communities in subseafloor sediments reported that abundance and diversity decrease with sediment depth age, microbes dominating at tend to be a subset the local seafloor community. However, existence geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic metatranscriptomic analyses hydrothermally heated, layers Guaymas Basin (Gulf California, Mexico) examine distribution activity patterns bacteria archaea along thermal, geochemical cell count gradients. We find composition metagenome-assembled genomes (MAGs), dominated by numerous lineages Chloroflexota Thermoproteota, correlate biogeochemical parameters as long temperatures remain moderate, but downcore increasing beyond ca. 45 ºC override other factors. Consistently, MAG size temperature, indicating winnowing subsurface biosphere. By contrast, specific archaeal MAGs within Thermoproteota Hadarchaeota increase relative recruitment transcriptome reads towards deeper, hotter sediments, marking transition specialized deep, hot

Language: Английский

Citations

11
Distribution and bioaccumulation of per- and polyfluoroalkyl substances (PFASs) in the Kuroshio Extension region of Northwest Pacific Ocean DOI
Yanhui Dai,

Guopeng Tian,

Hao Wang

et al.

Water Research, Journal Year: 2024, Volume and Issue: 265, P. 122256 - 122256

Published: Aug. 12, 2024

Language: Английский

Citations

4