Evidences for microbial precipitation of calcite in speleothems from Krem Syndai in Jaintia Hills, Meghalaya, India

Sushmitha Baskar (Corresponding Author), Joyanto Routh, Ramanathan Baskar, Abhinav Kumar, Hanna Miettinen, Merja Itävaara

Research output: Contribution to journalArticleScientificpeer-review

5 Citations (Scopus)

Abstract

Speleothems from Krem Syndai, Meghalaya in Northeast India were studied for their microbial diversity using 16S rDNA-based phylogenetic approach and conventional microbiological techniques along with geochemistry, mineralogy and in vitro experiments to understand participation of microorganisms in CaCO3 precipitation. Speleothems imaged by scanning electron microscopy showed round coccoid-like, sporangia-like and spinose calcified structures, numerous broken cocci shells with spotted interiors inside a calcite crystal, honeycomb long reticulate, smooth, flat, twisted, ribbon-like, tubular, beaded, microbe-mineralized filaments and extracellular polymeric substances (EPS). Fourier spectroscopy indicated the presence of various organic compounds. d13C and d18O isotopic ratios of speleothems ranged from -4.65 to -7.34% and -3.06 to -6.80%, respectively. Total number of microbial cells using SYBR Gold was high. Fluorescence in situ hybridization (FISH) indicated approximately 3 * 105 to 5 * 105 cells g sed-1 in the speleothems out of which the number of microbes belonging to Eubacteria ranged from 1.8 * 105 to 3.6 * 105 cells, g sed-1. FISH showed ~45% active microbial cells of the total cell number in samples. DNA-based high-throughput amplicon sequencing revealed 19 bacterial phyla in the speleothem. Approximately 42% of the sequences were similar to Proteobacteria (Alphaproteobacteria: 22.4%, Betaproteobacteria: 8.9%, Gammaproteobacteria: 8.6%). Sequences similar to Nitrospiraceae (22.8%) had the highest proportion of sequences belonging to a single family. Bacterial strains isolated from the speleothems raised alkalinity and precipitated calcite in the laboratory cultures which was confirmed by X-ray diffraction (XRD) analyses. These isolates belonged to Bacillus spp., Actinomycetes spp., Streptomyces spp., Pseudomonas spp., Micrococcus spp., Staphylococcus spp., Xanthobacter spp. and Arthrobacter spp. Overall, the results showed unequivocal evidence of bacterial fingerprints during CaCO3 precipitation in the cave.
Original languageEnglish
Pages (from-to)906-933
JournalGeomicrobiology Journal
Volume33
Issue number10
DOIs
Publication statusPublished - 2016
MoE publication typeA1 Journal article-refereed

Fingerprint

speleothem
Calcium Carbonate
India
calcite
Fluorescence
Fluorescence In Situ Hybridization
Caves
Geochemistry
Mineralogy
Xanthobacter
Bacilli
Alkalinity
Cell Count
Ribosomal DNA
Microbiological Techniques
Sporangia
Organic compounds
Gold
Microorganisms
Betaproteobacteria

Keywords

  • Cave
  • speleothem
  • geomicrobiology
  • biocalcification

Cite this

Baskar, Sushmitha ; Routh, Joyanto ; Baskar, Ramanathan ; Kumar, Abhinav ; Miettinen, Hanna ; Itävaara, Merja. / Evidences for microbial precipitation of calcite in speleothems from Krem Syndai in Jaintia Hills, Meghalaya, India. In: Geomicrobiology Journal. 2016 ; Vol. 33, No. 10. pp. 906-933.
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title = "Evidences for microbial precipitation of calcite in speleothems from Krem Syndai in Jaintia Hills, Meghalaya, India",
abstract = "Speleothems from Krem Syndai, Meghalaya in Northeast India were studied for their microbial diversity using 16S rDNA-based phylogenetic approach and conventional microbiological techniques along with geochemistry, mineralogy and in vitro experiments to understand participation of microorganisms in CaCO3 precipitation. Speleothems imaged by scanning electron microscopy showed round coccoid-like, sporangia-like and spinose calcified structures, numerous broken cocci shells with spotted interiors inside a calcite crystal, honeycomb long reticulate, smooth, flat, twisted, ribbon-like, tubular, beaded, microbe-mineralized filaments and extracellular polymeric substances (EPS). Fourier spectroscopy indicated the presence of various organic compounds. d13C and d18O isotopic ratios of speleothems ranged from -4.65 to -7.34{\%} and -3.06 to -6.80{\%}, respectively. Total number of microbial cells using SYBR Gold was high. Fluorescence in situ hybridization (FISH) indicated approximately 3 * 105 to 5 * 105 cells g sed-1 in the speleothems out of which the number of microbes belonging to Eubacteria ranged from 1.8 * 105 to 3.6 * 105 cells, g sed-1. FISH showed ~45{\%} active microbial cells of the total cell number in samples. DNA-based high-throughput amplicon sequencing revealed 19 bacterial phyla in the speleothem. Approximately 42{\%} of the sequences were similar to Proteobacteria (Alphaproteobacteria: 22.4{\%}, Betaproteobacteria: 8.9{\%}, Gammaproteobacteria: 8.6{\%}). Sequences similar to Nitrospiraceae (22.8{\%}) had the highest proportion of sequences belonging to a single family. Bacterial strains isolated from the speleothems raised alkalinity and precipitated calcite in the laboratory cultures which was confirmed by X-ray diffraction (XRD) analyses. These isolates belonged to Bacillus spp., Actinomycetes spp., Streptomyces spp., Pseudomonas spp., Micrococcus spp., Staphylococcus spp., Xanthobacter spp. and Arthrobacter spp. Overall, the results showed unequivocal evidence of bacterial fingerprints during CaCO3 precipitation in the cave.",
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Evidences for microbial precipitation of calcite in speleothems from Krem Syndai in Jaintia Hills, Meghalaya, India. / Baskar, Sushmitha (Corresponding Author); Routh, Joyanto; Baskar, Ramanathan; Kumar, Abhinav; Miettinen, Hanna; Itävaara, Merja.

In: Geomicrobiology Journal, Vol. 33, No. 10, 2016, p. 906-933.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Evidences for microbial precipitation of calcite in speleothems from Krem Syndai in Jaintia Hills, Meghalaya, India

AU - Baskar, Sushmitha

AU - Routh, Joyanto

AU - Baskar, Ramanathan

AU - Kumar, Abhinav

AU - Miettinen, Hanna

AU - Itävaara, Merja

PY - 2016

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N2 - Speleothems from Krem Syndai, Meghalaya in Northeast India were studied for their microbial diversity using 16S rDNA-based phylogenetic approach and conventional microbiological techniques along with geochemistry, mineralogy and in vitro experiments to understand participation of microorganisms in CaCO3 precipitation. Speleothems imaged by scanning electron microscopy showed round coccoid-like, sporangia-like and spinose calcified structures, numerous broken cocci shells with spotted interiors inside a calcite crystal, honeycomb long reticulate, smooth, flat, twisted, ribbon-like, tubular, beaded, microbe-mineralized filaments and extracellular polymeric substances (EPS). Fourier spectroscopy indicated the presence of various organic compounds. d13C and d18O isotopic ratios of speleothems ranged from -4.65 to -7.34% and -3.06 to -6.80%, respectively. Total number of microbial cells using SYBR Gold was high. Fluorescence in situ hybridization (FISH) indicated approximately 3 * 105 to 5 * 105 cells g sed-1 in the speleothems out of which the number of microbes belonging to Eubacteria ranged from 1.8 * 105 to 3.6 * 105 cells, g sed-1. FISH showed ~45% active microbial cells of the total cell number in samples. DNA-based high-throughput amplicon sequencing revealed 19 bacterial phyla in the speleothem. Approximately 42% of the sequences were similar to Proteobacteria (Alphaproteobacteria: 22.4%, Betaproteobacteria: 8.9%, Gammaproteobacteria: 8.6%). Sequences similar to Nitrospiraceae (22.8%) had the highest proportion of sequences belonging to a single family. Bacterial strains isolated from the speleothems raised alkalinity and precipitated calcite in the laboratory cultures which was confirmed by X-ray diffraction (XRD) analyses. These isolates belonged to Bacillus spp., Actinomycetes spp., Streptomyces spp., Pseudomonas spp., Micrococcus spp., Staphylococcus spp., Xanthobacter spp. and Arthrobacter spp. Overall, the results showed unequivocal evidence of bacterial fingerprints during CaCO3 precipitation in the cave.

AB - Speleothems from Krem Syndai, Meghalaya in Northeast India were studied for their microbial diversity using 16S rDNA-based phylogenetic approach and conventional microbiological techniques along with geochemistry, mineralogy and in vitro experiments to understand participation of microorganisms in CaCO3 precipitation. Speleothems imaged by scanning electron microscopy showed round coccoid-like, sporangia-like and spinose calcified structures, numerous broken cocci shells with spotted interiors inside a calcite crystal, honeycomb long reticulate, smooth, flat, twisted, ribbon-like, tubular, beaded, microbe-mineralized filaments and extracellular polymeric substances (EPS). Fourier spectroscopy indicated the presence of various organic compounds. d13C and d18O isotopic ratios of speleothems ranged from -4.65 to -7.34% and -3.06 to -6.80%, respectively. Total number of microbial cells using SYBR Gold was high. Fluorescence in situ hybridization (FISH) indicated approximately 3 * 105 to 5 * 105 cells g sed-1 in the speleothems out of which the number of microbes belonging to Eubacteria ranged from 1.8 * 105 to 3.6 * 105 cells, g sed-1. FISH showed ~45% active microbial cells of the total cell number in samples. DNA-based high-throughput amplicon sequencing revealed 19 bacterial phyla in the speleothem. Approximately 42% of the sequences were similar to Proteobacteria (Alphaproteobacteria: 22.4%, Betaproteobacteria: 8.9%, Gammaproteobacteria: 8.6%). Sequences similar to Nitrospiraceae (22.8%) had the highest proportion of sequences belonging to a single family. Bacterial strains isolated from the speleothems raised alkalinity and precipitated calcite in the laboratory cultures which was confirmed by X-ray diffraction (XRD) analyses. These isolates belonged to Bacillus spp., Actinomycetes spp., Streptomyces spp., Pseudomonas spp., Micrococcus spp., Staphylococcus spp., Xanthobacter spp. and Arthrobacter spp. Overall, the results showed unequivocal evidence of bacterial fingerprints during CaCO3 precipitation in the cave.

KW - Cave

KW - speleothem

KW - geomicrobiology

KW - biocalcification

U2 - 10.1080/01490451.2015.1127447

DO - 10.1080/01490451.2015.1127447

M3 - Article

VL - 33

SP - 906

EP - 933

JO - Geomicrobiology Journal

JF - Geomicrobiology Journal

SN - 0149-0451

IS - 10

ER -