Bacterial and Archaeal Communities in Recycling Effluents from a Bauxite Flotation Plant

AbstractRecycling effluent has become a bottleneck and an environmental risk associated with the regular production of bauxite via flotation and the sustainable development of the aluminum industry in China. To find a practical direction for biotreatment, the bacterial and archaeal communities in recycling effluents containing concentrate and tailings from bauxite flotation plants were investigated by a metagenomic sequencing method in association with the evaluated geochemical properties. The results showed that Paracoccus, Desulfomicrobium, Exiguobacterium, Tindallia, Ercella and Anoxynatronum were the primary bacterial genera and Methanothrix, Methanobacterium, Nitrososphaera and Methanosarcina were the dominant archaeal genera. Upon combining the microbial diversity and the geochemical properties of the two sample types, the microbial community containing Desulfomicrobium, Paracoccus, Tindallia, Methanobacterium, Methanothrix and Nitrososphaera was better adapted to the biodegradation of flotation collectors, and the microbial community consisting of Paracoccus, Exiguobacterium, Methanothrix and Methanobacterium was more efficient at hydrolyzed polyacrylamide (HPAM) biodegradation. In addition, a large proportion of unclassified OTUs has indicated that recycling effluent is a worthy resource for isolating new strains from the Firmicutes phylum.

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Distinctive prokaryotic microbiomes in sympatric plant roots from a Yucatan cenote

BMC Research Notes ◽

10.1186/s13104-021-05746-x ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Alejandra Escobar-Zepeda ◽

Patricia Rosas-Escobar ◽

Laura Marquez Valdelamar ◽

Patricia de la Torre ◽

Laila P. Partida-Martinez ◽

...

Keyword(s):

Microbial Community ◽

Dna Barcoding ◽

Genomic Dna ◽

Plant Roots ◽

Ecological Interactions ◽

Prokaryotic Community ◽

Prokaryotic Diversity ◽

Bacterial And Archaeal Communities ◽

Reported Data ◽

Archaeal Communities

Abstract Objective Cenotes are flooded caves in Mexico’s Yucatan peninsula. Many cenotes are interconnected in an underground network of pools and streams forming a vast belowground aquifer across most of the peninsula. Many plants in the peninsula grow roots that reach the cenotes water and live submerged in conditions similar to hydroponics. Our objective was to study the microbial community associated with these submerged roots of the Sac Actun cenote. We accomplished this objective by profiling the root prokaryotic community using 16S rRNA gene amplification and sequencing. Results We identified plant species by DNA barcoding the total genomic DNA of each root. We found a distinctive composition of the root and water bacterial and archaeal communities. Prokaryotic diversity was higher in all plant roots than in the surrounding freshwater, suggesting that plants in the cenotes may attract and select microorganisms from soil and freshwater, and may also harbor vertically transmitted lineages. The reported data are of interest for studies targeting biodiversity in general and root-microbial ecological interactions specifically.

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The global-scale distributions of soil protists and their contributions to belowground systems

Science Advances ◽

10.1126/sciadv.aax8787 ◽

2020 ◽

Vol 6 (4) ◽

pp. eaax8787 ◽

Cited By ~ 21

Author(s):

Angela M. Oliverio ◽

Stefan Geisen ◽

Manuel Delgado-Baquerizo ◽

Fernando T. Maestre ◽

Benjamin L. Turner ◽

...

Keyword(s):

Amplicon Sequencing ◽

Global Scale ◽

Arid Ecosystems ◽

Soil Microbiome ◽

Metagenomic Sequencing ◽

Soil Functioning ◽

Shotgun Metagenomic Sequencing ◽

Bacterial And Archaeal Communities ◽

Soil Protists ◽

Archaeal Communities

Protists are ubiquitous in soil, where they are key contributors to nutrient cycling and energy transfer. However, protists have received far less attention than other components of the soil microbiome. We used amplicon sequencing of soils from 180 locations across six continents to investigate the ecological preferences of protists and their functional contributions to belowground systems. We complemented these analyses with shotgun metagenomic sequencing of 46 soils to validate the identities of the more abundant protist lineages. We found that most soils are dominated by consumers, although parasites and phototrophs are particularly abundant in tropical and arid ecosystems, respectively. The best predictors of protist composition (primarily annual precipitation) are fundamentally distinct from those shaping bacterial and archaeal communities (namely, soil pH). Some protists and bacteria co-occur globally, highlighting the potential importance of these largely undescribed belowground interactions. Together, this study allowed us to identify the most abundant and ubiquitous protists living in soil, with our work providing a cross-ecosystem perspective on the factors structuring soil protist communities and their likely contributions to soil functioning.

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Environmental Filtering by pH and Salinity Jointly Drives Prokaryotic Community Assembly in Coastal Wetland Sediments

Frontiers in Marine Science ◽

10.3389/fmars.2021.792294 ◽

2022 ◽

Vol 8 ◽

Author(s):

Huang Yu ◽

Qiuping Zhong ◽

Yisheng Peng ◽

Xiafei Zheng ◽

Fanshu Xiao ◽

...

Keyword(s):

Microbial Community ◽

Community Assembly ◽

Coastal Wetland ◽

Environmental Filtering ◽

Large Network ◽

Prokaryotic Community ◽

Bacterial And Archaeal Communities ◽

Microbial Community Assembly ◽

Archaeal Communities ◽

Offshore Sediments

Understanding the microbial community assembly is an essential topic in microbial ecology. Coastal wetlands are an important blue carbon sink, where microbes play a key role in biogeochemical cycling of nutrients and energy transformation. However, the drivers controlling the distribution patterns and assembly of bacterial and archaeal communities in coastal wetland are unclear. Here we examined the diversity, co-occurrence network, assembly processes and environmental drivers of bacterial and archaeal communities from inshore to offshore sediments by the sequencing of 16S rRNA gene amplicons. The value of α- and β-diversity of bacterial and archaeal communities generally did not change significantly (P > 0.05) between offshore sites, but changed significantly (P < 0.05) among inshore sites. Sediment pH and salinity showed significant effects on the diversity and keystone taxa of bacterial and archaeal communities. The bacterial and archaeal co-occurrence networks were inextricably linked with pH and salinity to formed the large network nodes, suggesting that they were the key factors to drive the prokaryotic community. We also identified that heterogeneous and homogeneous selection drove the bacterial and archaeal community assembly, while the two selections became weaker from offshore sites to inshore sites, suggesting that deterministic processes were more important in offshore sites. Overall, these results suggested that the environmental filtering of pH and salinity jointly governed the assembly of prokaryotic community in offshore sediments. This study advances our understanding of microbial community assembly in coastal wetland ecosystems.

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Lake trophic states shape microbial community structure in sediments

10.5194/egusphere-egu2020-9772 ◽

2020 ◽

Author(s):

Xingguo Han ◽

Carsten Schubert ◽

Annika Fiskal ◽

Nathalie Dubois ◽

Mark Lever

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Lake Sediments ◽

Microbial Community Structure ◽

Trophic State ◽

Oligotrophic Lake ◽

Eutrophic Lakes ◽

Bacterial And Archaeal Communities ◽

Archaeal Communities

Lake sediments are globally important carbon sinks, and play a critical role in the global carbon cycle. Although the fate of organic carbon in lake sediments depends mostly on sedimentary microorganisms, the environmental controls on the microbial community structure in lake sediments are still poorly understood.Here we investigate the relationships of lake trophic state, sediment redox chemistry, sediment organic matter (OM) sources and microbial community structure in sediment records across five lakes with different eutrophication histories and trophic states in central Switzerland. Our results show that, across all five lakes, bacterial and archaeal communities based on 16S rRNA gene sequencing analyses show similar sediment depth-dependent zonations at the phylum- and class-level, which appears to be primarily driven by vertical distributions of electron acceptors and secondarily by differences in the contributions of aquatic and terrestrial OM revealed by biomarkers. Yet, there are clear differences in microbial communities between lakes, most notably the higher abundances of putatively aerobic nitrifying Bacteria (Nitrospirae) and Archaea (Marine Group I, Thaumarchaeota) in anoxic sediments of oligotrophic Lake Lucerne. Furthermore, at the level of Zero-radius Operational Taxonomic Unit (ZOTU), eutrophication-related trends are more pronounced, in which microbial communities in the sediments of eutrophic lakes are more similar and share more ZOTUs with each other than with the oligotrophic lake. Notably, deep sediment layers of presently eutrophic lakes that were deposited prior to the era of eutrophication show high similarities in bacterial communities to equivalent depths in the oligotrophic lake. By contrast, archaeal communities are clearly differentiated according to trophic state only in recently deposited sediment layers, and independent of trophic state converge toward high similarities over time.Our study indicates a significant role of trophic status in driving lacustrine sediment microbial communities and reveals fundamental differences in the temporal responses of bacterial and archaeal communities to anthropogenic eutrophication.

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Restoration Efficacy of Picea likiangensis var. rubescens Rehder & E. H. Wilson Plantations on the Soil Microbial Community Structure and Function in a Subalpine Area

Microorganisms ◽

10.3390/microorganisms9061145 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1145

Author(s):

Jixin Cao ◽

Songlin Shi ◽

Hong Pan ◽

Zhan Chen ◽

He Shang

Keyword(s):

Microbial Community ◽

Soil Microbial Community ◽

Coniferous Forest ◽

Structure And Function ◽

Tree Species Composition ◽

Soil Microbial Community Structure ◽

Soil Microbial ◽

Bacterial And Archaeal Communities ◽

And Function ◽

Archaeal Communities

The knowledge concerning the relationship between vegetation restoration and soil microorganisms is limited, especially at high altitudes. In order to evaluate the restoration efficacy of the reforestation on the soil microbial community, we have examined vegetation composition, edaphic properties and structure and function of different soil microbial groups in two different aged (25- and 40-year-old) Picea likiangensis var. rubescens Rehder & E. H. Wilson (P. rubescens) plantations and the primeval coniferous forest (PCF) dominated by Abies squamata Masters by plot-level inventories and sampling in western Sichuan Province, China. Our results suggested that only the fungal samples in 25-year-old P. rubescens plantation could be distinguished from those in the PCF in both structure and function. The structure and function of the fungal community recovered relatively slowly compared with bacterial and archaeal communities. In addition to the soil chemical properties and tree species composition, the shrub composition was also a key factor influencing the soil microbial community. The P. rubescens plantations were conducive to restoring the soil microbial community in both structure and function. However, there were uncertainties in the variations of the bacterial and archaeal communities with increasing the P. rubescens plantation age.

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Isolation and identification of a novel bacterium, Pseudomonas sp. ZyL-01, involved in the biodegradation of CL-20

AMB Express ◽

10.1186/s13568-020-01136-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Zhiyong Liu ◽

Kai Dang ◽

Cunzhi Li ◽

Junhong Gao ◽

Hong Wang ◽

...

Keyword(s):

Microbial Community ◽

Environmental Fate ◽

Draft Genome ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Community Diversity ◽

Functional Enrichment ◽

Metagenomic Sequencing ◽

Isolation And Identification ◽

Novel Bacterium

Abstract Hexanitrohexaazaisowurtzitane (CL-20) is a compound with a polycyclic cage and an N-nitro group that has been shown to play an unfavorable role in environmental fate, biosafety, and physical health. The aim of this study was to isolate the microbial community and to identify a single microbial strain that can degrade CL-20 with desirable efficiency. Metagenomic sequencing methods were performed to investigate the dynamic changes in the composition of the community diversity. The most varied genus among the microbial community was Pseudomonas, which increased from 1.46% to 44.63% during the period of incubation (MC0–MC4). Furthermore, the new strain was isolated and identified from the activated sludge by bacterial morphological and 16s rRNA sequencing analyses. The CL-20 concentrations decreased by 75.21 μg/mL and 74.02 μg/mL in 48 h by MC4 and Pseudomonas sp. ZyL-01, respectively. Moreover, ZyL-01 could decompose 98% CL-20 of the real effluent in 14 day’s incubation with the glucose as carbon source. Finally, a draft genome sequence was obtained to predict possible degrading enzymes involved in the biodegradation of CL-20. Specifically, 330 genes that are involved in energy production and conversion were annotated by Gene Ontology functional enrichment analysis, and some of these candidates may encode enzymes that are responsible for CL-20 degradation. In summary, our studies indicate that microbes might be a valuable biological resource for the treatment of environmental contamination caused by CL-20 and that Pseudomonas sp. ZyL-01 might be a promising candidate for eradicating CL-20 to achieve a more biosafe environment and improve public health.

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Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

Microorganisms ◽

10.3390/microorganisms9020211 ◽

2021 ◽

Vol 9 (2) ◽

pp. 211

Author(s):

Jie Gao ◽

Miao Liu ◽

Sixue Shi ◽

Ying Liu ◽

Yu Duan ◽

...

Keyword(s):

Microbial Community ◽

High Throughput Sequencing ◽

Carbon Fixation ◽

Microbial Community Composition ◽

Ecosystem Functions ◽

Microbial Composition ◽

Wetland Ecosystems ◽

Soil Microbial ◽

Geochemical Properties ◽

Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

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