Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds

Ghezzi, Daniele; Filippini, María; Cappelletti, Martina; Firrincieli, Andrea; Zannoni, Davide; Gargini, Alessandro; Fedi, Stefano

doi:10.1007/s11356-020-12236-3

Cited by 8 publications

(5 citation statements)

References 86 publications

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“…Hierarchical clustering and PCoA results show that chlorinated hydrocarbon pollution stress was the main driving factor of archaeal community structure. A field investigation has revealed that chlorinated aliphatic compounds can decrease microbial population richness and influence the composition and diversity of microbial communities [12]. In this study, hierarchical clustering and PCoA results show that chlorinated hydrocarbon pollution stress was the main driving factor of archaeal community structure, which is consistent with previous reports.…”

Section: Discussionsupporting

confidence: 92%

“…Although most environments are dominated by bacteria [10], archaea are more dominant under extreme conditions [11]. In an aquifer system contaminated with chlorinated aliphatic compounds, archaea were included in the top three microbial phyla of all samples [12]. The gene types and metabolic characteristics of archaea are different from those of bacteria [13,14].…”

Section: Introductionmentioning

confidence: 99%

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Structure and Assembly Mechanism of Archaeal Communities in Deep Soil Contaminated by Chlorinated Hydrocarbons

Fan

Liu

et al. 2023

Sustainability

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Chlorinated hydrocarbons are typical organic pollutants in contaminated sites, and microbial remediation technology has attracted more and more attention. To study the structural characteristics and assembly mechanism of the archaeal community in chlorinated hydrocarbon-contaminated soil, unsaturated-zone soil within 2~10 m was collected. Based on high-throughput sequencing technology, the archaeal community was analyzed, and the main drivers, environmental influencing factors, and assembly mechanisms were revealed. The results showed that chlorinated hydrocarbon pollution altered archaeal community structure. The archaeal community composition was significantly correlated with trichloroethylene (r = 0.49, p = 0.001), chloroform (r = 0.60, p = 0.001), pH (r = 0.27, p = 0.036), sulfate (r = 0.21, p = 0.032), and total carbon (r = 0.23, p = 0.041). Under pollution stress, the relative abundance of Thermoplasmatota increased to 25.61%. Deterministic processes increased in the heavily polluted soil, resulting in reduced species richness, while positive collaboration among surviving species increased to 100%. These results provide new insights into the organization of archaeal communities in chlorinated hydrocarbon-contaminated sites and provide a basis for remediation activities.

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Section: Discussionsupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Structure and Assembly Mechanism of Archaeal Communities in Deep Soil Contaminated by Chlorinated Hydrocarbons

Fan

Liu

et al. 2023

Sustainability

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“…The orders Nitrospirales ( Nitrospira genus), 0319-7L14 (of Actinobacteriota phylum), and Nitrosopumilales ( Nitrosarchaeum genus), that are dominant in the apical part, were strongly correlated with condensed organic compounds, probably due to their ability to degrade these recalcitrant compounds [ 58 , 59 ]. Diverse microbial orders abundant in the core part were correlated with aromatic, lignin, and polysaccharides and some of them, i.e., Burkholderiales (mainly of Massilia genus), Kryptoniales (family BSV26), Anaerolineales , and Rokubacteriales , are known to degrade aromatic and lignin compounds in different ecosystems (e.g., soil, water, and sediments) [ 39 , 60 – 62 ]. Finally, the Nitrosococcales (genus wb1-P19) present in the lateral part and bedrock are correlated with fresh organic matter (peptides, fatty acids, hydroaromatics, and lipids), which are typically associated with active microbial metabolism.…”

Section: Discussionmentioning

confidence: 99%

“…The demultiplexed and primer-clipped reads were trimmed based on quality and length, and further dereplicated, denoised, merged, and checked for chimeras by using Qiime2 version 2018.4 [ 38 ]. Reads were processed into Amplicon Sequence Variants (ASVs) using the DADA2 package version 1.14 as described in [ 39 ]. The taxonomic assignment of the resulting ASVs was performed by querying the ASVs against SILVA SSU database version r138.1 [ 40 ].…”

Section: Methodsmentioning

confidence: 99%

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

Ghezzi,

Jiménez-Morillo,

Foschi

et al. 2024

Environmental Microbiome

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Background Moonmilk represents complex secondary structures and model systems to investigate the interaction between microorganisms and carbonatic rocks. Grotta Nera is characterized by numerous moonmilk speleothems of exceptional size hanging from the ceiling, reaching over two meters in length. In this work we combined microbiological analyses with analytical pyrolysis and carbon stable isotope data to determine the molecular composition of these complex moonmilk structures as well as the composition of the associated microbiota. Results Three moonmilk structures were dissected into the apical, lateral, and core parts, which shared similar values of microbial abundance, richness, and carbon isotopes but different water content, microbiota composition, and organic matter. Moonmilk parts/niches showed higher values of microbial biomass and biodiversity compared to the bedrock (not showing moonmilk development signs) and the waters (collected below dripping moonmilk), indicating the presence of more complex microbial communities linked to carbonate rock interactions and biomineralization processes. Although each moonmilk niche was characterized by a specific microbiota as well as a distinct organic carbon profile, statistical analyses clustered the samples in two main groups, one including the moonmilk lateral part and the bedrock and the other including the core and apical parts of the speleothem. The organic matter profile of both these groups showed two well-differentiated organic carbon groups, one from cave microbial activity and the other from the leaching of vascular plant litter above the cave. Correlation between organic matter composition and microbial taxa in the different moonmilk niches were found, linking the presence of condensed organic compounds in the apical part with the orders Nitrospirales and Nitrosopumilales, while different taxa were correlated with aromatic, lignin, and polysaccharides in the moonmilk core. These findings are in line with the metabolic potential of these microbial taxa suggesting how the molecular composition of the preserved organic matter drives the microbiota colonizing the different moonmilk niches. Furthermore, distinct bacterial and archaeal taxa known to be involved in the metabolism of inorganic nitrogen and C1 gases (CO2 and CH4) (Nitrospira, Nitrosopumilaceae, Nitrosomonadaceae, Nitrosococcaceae, and novel taxa of Methylomirabilota and Methanomassiliicoccales) were enriched in the core and apical parts of the moonmilk, probably in association with their contribution to biogeochemical cycles in Grotta Nera ecosystem and moonmilk development. Conclusions The moonmilk deposits can be divided into diverse niches following oxygen and water gradients, which are characterized by specific microbial taxa and organic matter composition originating from microbial activities or deriving from soil and vegetation above the cave. The metabolic capacities allowing the biodegradation of complex polymers from the vegetation above the cave and the use of inorganic nitrogen and atmospheric gases might have fueled the development of complex microbial communities that, by interacting with the carbonatic rock, led to the formation of these massive moonmilk speleothems in Grotta Nera.

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“…To provide amplicon for Illumina MiSeq analysis, the total DNA was amplified for the V4-V5 hypervariable region of 16S rRNA gene with universal forward 515F (5′-Illumina overhang-GTGYCAGCMGCCGC GGTA-3′) and reverse 907R (5′-Illumina overhang-CCGTCAATTC MTTTRAGTTT-3′) primers (IDT DNA Technologies). The PCR reaction mixture contained 10 ng of total DNA, 1x Takara Ex Taq buffer with MgCl 2 (10x, Takara Bio Inc., Tokyo, Japan), dNTP mix 200 μM, primers 500 nM, and Takara Ex Taq Polymerase 0.5 U and water (Lichrosolv ® ; Merck, Darmstadt, Germany) up to a total volume of 50 μl (Ghezzi et al, 2021a). Amplification reactions were carried out under the following thermocycling conditions: 95°C for 3 min, 30 cycles of 95°C for 30 s, 55°C for 30 s, 72°C for 30 s, with a final extension at 72°C for 5 min.…”

Section: Dna Extraction V4-v5 16s Rrna Gene Amplification and Sequencingmentioning

confidence: 99%

Insights into the microbial life in silica-rich subterranean environments: microbial communities and ecological interactions in an orthoquartzite cave (Imawarì Yeuta, Auyan Tepui, Venezuela)

et al. 2022

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Microbial communities inhabiting caves in quartz-rich rocks are still underexplored, despite their possible role in the silica cycle. The world’s longest orthoquartzite cave, Imawarì Yeuta, represents a perfect arena for the investigation of the interactions between microorganisms and silica in non-thermal environments due to the presence of extraordinary amounts of amorphous silica speleothems of different kinds. In this work, the microbial diversity of Imawarì Yeuta was dissected by analyzing nineteen samples collected from different locations representative of different silica amorphization phases and types of samples. Specifically, we investigated the major ecological patterns in cave biodiversity, specific taxa enrichment, and the main ecological clusters through co-occurrence network analysis. Water content greatly contributed to the microbial communities’ composition and structures in the cave leading to the sample clustering into three groups DRY, WET, and WATER. Each of these groups was enriched in members of Actinobacteriota, Acidobacteriota, and Gammaproteobacteria, respectively. Alpha diversity analysis showed the highest value of diversity and richness for the WET samples, while the DRY group had the lowest. This was accompanied by the presence of correlation patterns including either orders belonging to various phyla from WET samples or orders belonging to the Actinobacteriota and Firmicutes phyla from DRY group samples. The phylogenetic analysis of the dominant species in WET and DRY samples showed that Acidobacteriota and Actinobacteriota strains were affiliated with uncultured bacteria retrieved from various oligotrophic and silica/quartz-rich environments, not only associated with subterranean sites. Our results suggest that the water content greatly contributes to shaping the microbial diversity within a subterranean quartzite environment. Further, the phylogenetic affiliation between Imawarì Yeuta dominant microbes and reference strains retrieved from both surface and subsurface silica- and/or CO2/CO-rich environments, underlines the selective pressure applied by quartz as rock substrate. Oligotrophy probably in association with the geochemistry of silica/quartz low pH buffering activity and alternative energy sources led to the colonization of specific silica-associated microorganisms. This study provides clues for a better comprehension of the poorly known microbial life in subsurface and surface quartz-dominated environments.

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Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds

Cited by 8 publications

References 86 publications

Structure and Assembly Mechanism of Archaeal Communities in Deep Soil Contaminated by Chlorinated Hydrocarbons

Structure and Assembly Mechanism of Archaeal Communities in Deep Soil Contaminated by Chlorinated Hydrocarbons

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

Insights into the microbial life in silica-rich subterranean environments: microbial communities and ecological interactions in an orthoquartzite cave (Imawarì Yeuta, Auyan Tepui, Venezuela)

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