Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.

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Pseudomonas: A Major Bacteria in Heavy Metal Contaminated Soil of South-West Punjab, India

International Journal of Plant and Environment ◽

10.18811/ijpen.v5i01.5 ◽

2019 ◽

Vol 5 (01) ◽

pp. 26-32 ◽

Cited By ~ 1

Author(s):

Sanjeev Kumar ◽

Arindam Adhikary ◽

Rashmi Saini ◽

Pankaj Bhardwaj

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

16S Rrna ◽

16S Rrna Gene ◽

Contaminated Soil ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Pseudomonas Sp ◽

Rrna Gene Sequencing

Soil microflora is continuously changing with altered soil conditions. These soil alterations are a consequence of heavy metals entering and affecting every sphere of life. Heavy metals are not only hazardous for crops but also affect the soil microbial community. Soil bacteria with the potential of plant growth promotion and multiple metal resistances can be an instrument for crop improvement and heavy metal detoxification. In this study, predominant bacterial community associated with the heavy metal contaminated soil was studied using 16S rRNA gene sequencing in association with culture-based techniques. Elemental metal analysis of collected soil samples showed an elevated level of metal content in the soil. 16S rRNA gene analysis and phylogenetic analysis of 126 bacterial clones revealed the probable predominance of Pseudomonas (40.48%) followed by Flavisolibacter (13.49%). Based on morphological and biochemical characterization, nine Pseudomonas strains were selected from the soil and were further confirmed by 16S rRNA gene sequencing with 92%-100% similarity with Pseudomonas species. The minimum inhibitory concentration (MIC) and maximum tolerance capacity (MTC) of three essential metals Cu, Zn, and Fe were determined individually and in combinations. It was found that Zn is the most toxic metal among the three metals and the metal showed a synergistic effect in inhibiting microbial growth when used in combinations. Presence of three metal resistant/tolerant genes czcA, pcoA and copB were also determined in the isolated Pseudomonas sp. by PCR. The soil in this region has high concentrations of heavy metals. The indigenous Pseudomonas sp. has multiple metal resistances and can be used for bioremediation of heavy metals and microbe assisted phytoremediation.

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Effects of Heavy Metals/Metalloids and Soil Properties on Microbial Communities in Farmland in the Vicinity of a Metals Smelter

Frontiers in Microbiology ◽

10.3389/fmicb.2021.707786 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xuewu Hu ◽

Jianlei Wang ◽

Ying Lv ◽

Xingyu Liu ◽

Juan Zhong ◽

...

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

Soil Properties ◽

Microbial Communities ◽

Soil Ph ◽

Contaminated Soils ◽

High Throughput Sequencing ◽

Available Phosphorus ◽

Rrna Gene ◽

Multiple Heavy Metals

Microorganisms play a fundamental role in biogeochemical cycling and are highly sensitive to environmental factors, including the physiochemical properties of the soils and the concentrations of heavy metals/metalloids. In this study, high-throughput sequencing of the 16S rRNA gene was used to study the microbial communities of farmland soils in farmland in the vicinity of a lead–zinc smelter. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Gemmatimonadetes were the predominant phyla in the sites of interest. Sphingomonas, Gemmatimonas, Lysobacter, Flavisolibacter, and Chitinophaga were heavy metal-/metalloid-tolerant microbial groups with potential for bioremediation of the heavy metal/metalloid contaminated soils. However, the bacterial diversity was different for the different sites. The contents of heavy metal/metalloid species and the soil properties were studied to evaluate the effect on the soil bacterial communities. The Mantel test revealed that soil pH, total cadmium (T-Cd), and available arsenic played a vital role in determining the structure of the microbial communities. Further, we analyzed statistically the heavy metals/metalloids and the soil properties, and the results revealed that the microbial richness and diversity were regulated mainly by the soil properties, which correlated positively with organic matter and available nitrogen, while available phosphorus and available potassium were negatively correlated. The functional annotation of the prokaryotic taxa (FAPROTAX) method was used to predict the function of the microbial communities. Chemoheterotrophy and airborne chemoheterotrophy of the main microbial community functions were inhibited by soil pH and the heavy metals/metalloids, except in the case of available lead. Mantel tests revealed that T-Cd and available zinc were the dominant factors affecting the functions of the microbial communities. Overall, the research indicated that in contaminated soils, the presence of multiple heavy metals/metalloids, and the soil properties synergistically shaped the structure and function of the microbial communities.

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Shift of bacterial communities in heavy metal-contaminated agricultural land during a remediation process

PLoS ONE ◽

10.1371/journal.pone.0255137 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0255137

Author(s):

Chi-Chun Huang ◽

Chih-Ming Liang ◽

Ting-I Yang ◽

Jiann-Long Chen ◽

Wei-Kuang Wang

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

Community Structure ◽

Microbial Communities ◽

Contaminated Soil ◽

Bacterial Communities ◽

Soil Microbial Communities ◽

Soil Environment ◽

Soil Microbial ◽

Remediation Process

Anthropogenic activities accompanied by heavy metal waste threaten the environment. Heavy metal pollution alters the soil microbial community composition, and the microorganisms that adapt to this stress increase in abundance. The remediation process of contaminated soil not only reduces the concentration of heavy metals but also alters the bacterial communities. High-throughput 16S rDNA sequencing techniques were applied to understand the changes in soil microbial communities. Using the remediation approach of the soil mixing, the concentrations of heavy metals in the contaminated areas were diluted and the soil environment was changed. The change of soil environment as a disturbance contributed to the alteration of microbial diversity of the remediated areas. The pH and heavy metals (Cr, Cu, Ni, and Zn) were the most influential factors driving the changes in community structure. The bacterial community structure was significantly different among sample areas. The decrease of heavy metals in soil may be the important factors that changed the microbial composition. This study provides the better understanding of the changes in composition of microbial communities affected by the remediation process in heavy metal-contaminated soil.

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Evaluation of Acid Leaching on the Removal of Heavy Metals and Soil Fertility in Contaminated Soil

Journal of Chemistry ◽

10.1155/2018/5036581 ◽

2018 ◽

Vol 2018 ◽

pp. 1-8 ◽

Cited By ~ 4

Author(s):

Chen-Yao Chu ◽

Tzu-Hsing Ko

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

Seed Germination ◽

Soil Fertility ◽

Sequential Extraction ◽

Contaminated Soil ◽

Contaminated Soils ◽

Germination Rate ◽

Extraction Procedure ◽

Acid Leaching

Heavy metal-contaminated soils were leached with various acid reagents, and a series of treatments was assessed to understand soil fertility after acid leaching. Aqua regia digestion and a five-step sequential extraction procedure were applied to determine heavy metal distribution. The average total concentrations of Zn, Cd, Cu, and Pb for contaminated soil were 1334, 25, 263, and 525 mg·kg−1 based on the ICP/AES quantitative analysis. Other than Pb extracted by H2SO4, over 50% removal efficiency of other heavy metals was achieved. A five-step sequential extraction revealed that the bound-to-carbonate and bound-to-Fe-Mn oxides were the major forms of the heavy metals in the soil. The addition of organic manure considerably promoted soil fertility and increased soil pH after acid leaching. Seed germination experiments demonstrated that after acid leaching, the soil distinctly inhibited plant growth and the addition of manure enhanced seed germination rate from 35% to 84%. Furthermore, the procedure of soil turnover after acid leaching and manure addition greatly increased seed germination rate by 61% and shortened the initial germination time. Seed germination in untreated soil was superior to that in acid-leached soil, illustrating that the phytotoxic effect of acid leaching is more serious than that of heavy metals.

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Lichenological Practices for Monitoring Atmospheric Pollution and Climate Change in India

International Journal of Plant and Environment ◽

10.18811/ijpen.v5i03.0 ◽

2019 ◽

Vol 5 (03) ◽

pp. 170-185

Author(s):

Rajesh Bajpai ◽

C. P. Singh ◽

D. K. Upreti

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Soil Conditions ◽

Rrna Gene ◽

Pseudomonas Sp ◽

Rrna Gene Sequencing

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Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

10.1101/604314 ◽

2019 ◽

Author(s):

Philipp Rausch ◽

Malte Rühlemann ◽

Britt Hermes ◽

Shauni Doms ◽

Tal Dagan ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Microbial Composition ◽

Evolutionary Patterns ◽

Wide Range ◽

Taxonomic Groups ◽

And Function

AbstractBackgroundThe interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution and development of both players. These interdependencies inspired a new view of multicellular organisms as “metaorganisms”. The goal of the Collaborative Research Center “Origin and Function of Metaorganisms” is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants.MethodsIn order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon- and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample.ConclusionWhile 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods and that metagenomic shotgun results are largely dependent on the employed pipeline. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.

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Effects of Phosphate Rock on Absorption and Accumulation of Heavy Metals of Ryegrass in Heavy Metal Contaminated Soil

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.522-524.752 ◽

2014 ◽

Vol 522-524 ◽

pp. 752-757 ◽

Cited By ~ 1

Author(s):

Ying Zhe Wang ◽

Zhong Qiu Zhao ◽

Guang Yu Jiang

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

Perennial Ryegrass ◽

Significant Influence ◽

Contaminated Soil ◽

Contaminated Soils ◽

Phosphate Rock ◽

Particle Sizes ◽

Cu And Zn ◽

Soil Weight

The effects of phosphates rock (PR) with different particle sizes {D97<4.26 (the diameters of 97% of the particles are less than 4.26 µm.), <36.83, <71.12 and <101.43 µm} and different concentration (2.5% and 5% content of try soil weight) on immobilizing heavy metal-contaminated soils by a perennial ryegrass greenhouse experiment are conducted. Results indicate that remediation effect of applying 5% content is more significant than 2.5%. Ryegrass biomass in shoots in the former applying content is much larger than the latter and for both roots and shoots, PR reduces the absorption and accumulation of Pb, Cu and Zn, but no significant influence on Cd. While adding the same amount of different sizes of PR doesn’t show significant differences between these treatments. Pb content at 5% level of the finest size of PR is the minimum, decreased by 33% and 56% compared to the control in roots and shoots respectively, which was also suitable for Zn, decreased by 12.65% and 39.61% respectively.

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Alkalo-Thermophilic Microbial Diversity of the Tecozautla Geyser, México

10.21203/rs.3.rs-548312/v1 ◽

2021 ◽

Author(s):

Jesus Alberto Segovia-Cruz ◽

Valeria Souza ◽

Yuridia Mercado-Flores ◽

Miguel Angel Anducho-Reyes ◽

Genaro Vargas-Hernández ◽

...

Keyword(s):

16S Rrna ◽

Microbial Communities ◽

Software Package ◽

Microbial Mats ◽

Rrna Gene ◽

Thermal Systems ◽

Microbial Composition ◽

Salt Deposits ◽

The 16S Rrna Gene ◽

Storage Pools

Abstract Microbial mats have been studied in many thermal systems; the most iconic is Yellowstone. In Mexico, the information on microbial mats is scarce and therefore novel. In this research, the thermophilic microbial composition of samples from four areas of the Tecozautla geyser, Hidalgo, Mexico, was studied: sediments (GD), salt deposits (GA), and microbial mats (GB and GC). The samples were taken at the outlet of the geyser (94 °C) and in storage pools with temperatures of 61.5-65 °C. Sequencing of the 16S rRNA gene amplicons was carried out, obtaining 1,425,506 readings, and was analyzed through the Quantitative Insights Into Microbial Ecology software package version 2 (qiime2). 32 phyla were identified in the four samples being the most representative for the GA sample: Armatimonadetes, Chloroflexi, Cyanobacteria, and Thermi, with abundances of 46.35, 19.18, 3.27, and 1.82 %, respectively. For the GB sample, they were Proteobacteria, Bacteroidetes, Cyanobacteria, Spirochaetes, Thermi, and Firmicutes with abundances of 25.23, 22.04, 20.42, 12.31, 4.56, and 1.32 %, respectively. For the GC sample, abundances of 55.60, 9.85, 7.04, 7.01, and 6.15 % were observed for the phylum Chloroflexi, Armatimonadetes, Proteobacteria, Cyanobacteria, and Acidobacteria, respectively. Finally, for the GD sample, the most abundant phyla were Chloroflexi (36.10 %), Cyanobacteria (17.13 %), Armatimonadetes (15.59 %), Proteobacteria (5.45 %), and Nitrospirae with (3.21 %). The metabolic functionality of the microbial communities present in the samples was inferred using the 16S rRNA amplicons. This work represents the first report of the microbial communities present in the Tecozautla geyser.

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Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga.

F1000Research ◽

10.12688/f1000research.53779.2 ◽

2021 ◽

Vol 10 ◽

pp. 533

Author(s):

Mautusi Mitra ◽

Kevin Manoap-Anh-Khoa Nguyen ◽

Taylor Wayland Box ◽

Taylor Lynne Berry ◽

Megumi Fujita

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

16S Rrna ◽

16S Rrna Gene ◽

Chlamydomonas Reinhardtii ◽

Metal Tolerance ◽

Heavy Metal Tolerance ◽

Rrna Gene ◽

Isolation And Characterization ◽

Bacterial Cell Membrane

Background: Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.

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