Distinctive prokaryotic microbiomes in sympatric plant roots from a Yucatan cenote

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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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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Survival of the weakest in non-transitive asymmetric interactions among strains of E. coli

Nature Communications ◽

10.1038/s41467-020-19963-8 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Michael J. Liao ◽

Arianna Miano ◽

Chloe B. Nguyen ◽

Lin Chao ◽

Jeff Hasty

Keyword(s):

Microbial Community ◽

Cell Membrane ◽

Genomic Dna ◽

Dominant Species ◽

Protein Production ◽

Competitive Dynamics ◽

Hierarchical Organization ◽

Ecological Interactions ◽

E Coli ◽

Asymmetric Interactions

AbstractHierarchical organization in ecology, whereby interactions are nested in a manner that leads to a dominant species, naturally result in the exclusion of all but the dominant competitor. Alternatively, non-hierarchical competitive dynamics, such as cyclical interactions, can sustain biodiversity. Here, we designed a simple microbial community with three strains of E. coli that cyclically interact through (i) the inhibition of protein production, (ii) the digestion of genomic DNA, and (iii) the disruption of the cell membrane. We find that intrinsic differences in these three major mechanisms of bacterial warfare lead to an unbalanced community that is dominated by the weakest strain. We also use a computational model to describe how the relative toxin strengths, initial fractional occupancies, and spatial patterns affect the maintenance of biodiversity. The engineering of active warfare between microbial species establishes a framework for exploration of the underlying principles that drive complex ecological interactions.

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

10.1101/529958 ◽

2019 ◽

Author(s):

Xinxing Liu ◽

Yong-Hong Wu ◽

Xi Liu ◽

Wu Han-yan ◽

Jianping Xie ◽

...

Keyword(s):

Microbial Community ◽

Metagenomic Sequencing ◽

The Sustainable Development ◽

Geochemical Properties ◽

Regular Production ◽

Bacterial And Archaeal Communities ◽

Flotation Collectors ◽

The Aluminum Industry ◽

Hydrolyzed Polyacrylamide ◽

Archaeal Communities

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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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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Microeukaryotic and Prokaryotic Diversity of Anchialine Caves from Eastern Adriatic Sea Islands

Microbial Ecology ◽

10.1007/s00248-021-01760-5 ◽

2021 ◽

Author(s):

Katarina Kajan ◽

Neven Cukrov ◽

Nuša Cukrov ◽

Renée Bishop-Pierce ◽

Sandi Orlić

Keyword(s):

Microbial Community ◽

High Throughput Sequencing ◽

Adriatic Sea ◽

Salinity Gradient ◽

Biotic Interactions ◽

Prokaryotic Community ◽

Community Patterns ◽

Prokaryotic Diversity ◽

Anchialine Caves ◽

First Time

AbstractAnchialine ecosystems in the eastern Adriatic Sea are diverse both morphologically and biologically. In this study, for the first time, we explored the microeukaryotic and prokaryotic community of anchialine caves in the Mediterranean region using high-throughput sequencing. Four anchialine caves located on nearby islands with a well-pronounced salinity gradient were sampled at the surface freshwater area, halocline area, and seawater area. Sequencing revealed a surprisingly wide diversity of the microeukaryotic and prokaryotic community with the relative abundance of major phyla differing within the salinity gradient and between the caves. Interestingly, microeukaryotic and prokaryotic communities clustered into four groups based on location, pointing out that sampled anchialine caves have different microbial community patterns and high microbial endemism. Our results indicate that even with the halocline acting as a selecting barrier, the salinity is not the only community structuring factor. Despite the short geographical distance, the isolation of anchialine caves facilitated high microbial community adaptation and endemism. Our study suggests that anchialine caves represent reservoirs of new biodiversity, maintaining unique and complex microbial diversity influenced by biotic interactions and abiotic environmental conditions.

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Validating DNA Extraction Protocols for Bentonite Clay

mSphere ◽

10.1128/msphere.00334-19 ◽

2019 ◽

Vol 4 (5) ◽

Cited By ~ 3

Author(s):

Katja Engel ◽

Sara Coyotzi ◽

Melody A. Vachon ◽

Jennifer R. McKelvie ◽

Josh D. Neufeld

Keyword(s):

Microbial Community ◽

Nucleic Acid ◽

Nucleic Acids ◽

Dna Extraction ◽

Genomic Dna ◽

Bentonite Clay ◽

Dna Recovery ◽

Blocking Agents ◽

Clay Matrix ◽

Microbial Dna

ABSTRACT Bentonite clay is an integral component of the engineered barrier system of deep geological repositories (DGRs) that are planned for the long-term storage of high-level radioactive waste. Although nucleic acid extraction and analysis can provide powerful qualitative and quantitative data reflecting the presence, abundance, and functional potential of microorganisms within DGR materials, extraction of microbial DNA from bentonite clay is challenging due to the low biomass and adsorption of nucleic acids to the charged clay matrix. In this study, we used quantitative PCR, gel fingerprinting, and high-throughput sequencing of 16S rRNA gene amplicons to assess DNA extraction efficiency from natural MX-80 bentonite and the same material “spiked” with Escherichia coli genomic DNA. Extraction protocols were tested without additives and with casein and phosphate as blocking agents. Although we demonstrate improved DNA recovery by blocking agents at relatively high DNA spiking concentrations, at relatively low spiking concentrations, we detected a high proportion of contaminant nucleic acids from blocking agents that masked sample-specific microbial profile data. Because bacterial genomic DNA associated with casein preparations was insufficiently removed by UV treatment, casein is not recommended as an additive for DNA extractions from low-biomass samples. Instead, we recommend a kit-based extraction protocol for bentonite clay without additional blocking agents, as tested here and validated with multiple MX-80 bentonite samples, ensuring relatively high DNA recoveries with minimal contamination. IMPORTANCE Extraction of microbial DNA from MX-80 bentonite is challenging due to low biomass and adsorption of nucleic acid molecules to the charged clay matrix. Blocking agents improve DNA recovery, but their impact on microbial community profiles from low-biomass samples has not been characterized well. In this study, we evaluated the effect of casein and phosphate as blocking agents for quantitative recovery of nucleic acids from MX-80 bentonite. Our data justify a simplified framework for analyzing microbial community DNA associated with swelling MX-80 bentonite samples within the context of a deep geological repository for used nuclear fuel. This study is among the first to demonstrate successful extraction of DNA from Wyoming MX-80 bentonite.

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