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Sales, C. M.

Publications and source records attributed to Sales, C. M..

5 recordsLinked to original sources
bioRxiv2022

Evaluation of different strategies for efficient sporulation and germination of the MICP bacterium Lysinibacillus sphaericus strain MB284 (ATCC 13805)

Environmental harsh conditions are one of the main challenges to the survivability of bacteria during microbially induced calcium carbonate precipitation (MICP) process. Due to the high resistivity of endospores against inhospitable conditions in comparison with vegetative cells, different sporulation methods were applied to Lysinibacillus sphaericus strain MB284 by changing the environmental conditions to investigate the growth of germinated cells. It was found that the sporulation yield was more when both carbon source starvation and the thermal shock process were applied to this bacterium. In addition, extending the sporulation time of cells into the minimal medium at 2 {degrees}C for a couple of weeks had a great impact on improving the sporulation yield. Comparing the growth rate of germinated endospores in natural conditions (pH 7 and 25 {degrees}C) and harsh conditions (pH 12, temperature of -10 to 60 {degrees}C, salinity up to 100 g/l) showed that endospores generated by thermal shock are able to germinate in almost every inhospitable condition except at low pH ([~]3). Finally, exposing generated endospores before germination to harsh conditions (carbon source starving, high and low pH and temperature, and desiccation) for a nearly long period (to 100 days) showed that only low pH([~]3) had a negative effect on the germination process and bacterial growth curve that indicated endospore of strain MB284 can be an appropriate solution for the problem of the survivability of bioagents in MICP. These results will provide helpful information about preparing and applying endospores of L. sphaericus for crack healing in concrete. ImportanceIn the bio-self-healing process, bacterial cells are responsible for the production of calcium carbonate to fill cracks in the concrete. Since cracks can happen at any time, cells must survive under harsh conditions in concrete for a long period. This study for the first time investigates different endosporulation methods to find the best well-formed endospores for microbial-inducing calcium carbonate precipitation (MICP). This study shows that the endospores of strain MB284 formed by the thermal shock can survive under inhospitable conditions including different ranges of temperatures (-4 to 60 {degrees}C), pH (3 to 14), salinity (up to 100 g/l), and starvation for about 100 days. Furthermore, the bacterial growth rate and the kinetics of calcium carbonate production by germinated endospores and vegetative cells were similar to each other that indicate endospores of strain MB284 formed by the thermal shock method developed in this study are good candidates for the MICP process. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/508202v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1996544org.highwire.dtl.DTLVardef@1c75d69org.highwire.dtl.DTLVardef@1c5b728org.highwire.dtl.DTLVardef@17bb25d_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗
bioRxiv2022

Influence of culturing media components on the growth and microbial induced calcium carbonate precipitation (MICP) activity of Lysinibacillus sphaericus

In order to identify appropriate environmental conditions and media components that are either essential or that enhance its growth and Microbial induced calcium carbonate precipitation (MICP) activity, in this study, a series of experiments were conducted to investigate the effects of media components and oxygen conditions on the growth rate and MICP activity of Lysinibacillus sphaericus strain MB 284. From these experiments, it was observed that aerobic conditions could lead to increased calcium carbonate production and up to three times faster growth rates by strain MB284 when compared to anoxic conditions. It was also determined that considering the measured growth rate, final biomass concentration, ureolysis activity, amount of calcium carbonate precipitation, and cost of media components for designing undefined culture media for industrial applications, yeast extract is the most economically appropriate option. In our attempts to grow strain MB284 in urea, sucrose, and ammonium acetate as its sole carbon source in minimal media, it was observed it is auxotrophic and that casamino acids and casein are essential for its growth. Even though our experiments agree with the literature that the addition of urea enhances the growth and MICP activity of L. sphaericus, it was discovered that when the initial urea concentration was greater than 3 g/l, the growth rate of strain MB284 can be temporarily inhibited until enough cells and urease are produced. These results reveal that the growth and MICP activity of strain MB284 during its application for bio-self healing can be highly dependent on environmental and nutrient conditions. ImportanceO_LIAerobic conditions increase calcium carbonate production by strain MB284 C_LIO_LIyeast extract is the most economically appropriate option for industrial applications of MICP C_LIO_LILysinibacillus sphaericus strain MB 284 is auxotroph and casamino acids and casein are essential for its growth C_LIO_LIthe growth rate of strain MB284 can be temporarily inhibited with urea C_LI

bioengineering↗
bioRxiv2021

CuBi-MeAn Customized Pipeline for Metagenomic Data Analysis

1.Whole genome shotgun sequencing is a powerful to study microbial community is a given environment. Metagenomic binning offers a genome centric approach to study microbiomes. There are several tools available to process metagenomic data from raw reads to the interpretation there is still lack of standard approach that can be used to process the metagenomic data step by step. In this study CuBi-MeAn (Customizable Binning and Metagenomic Analysis) create a customizable and flexible processing pipeline, to process the metagenomic data and generate results for further interpretation. This study aims to perform metagenomic binning to enhance taxonomical classification, functional potentials, and interactions among microbial populations in environmental systems. This customized pipeline which is comprised of a series of genomic/metagenomic tools designed to recover better quality results and reliable interpretation of the system dynamics for the given systems. For this reason, a metagenomic data processing pipeline is developed to evaluate metagenomic data from three environmental engineering projects. The use of our pipeline was demonstrated and compared on three different datasets that were of different sizes, from different sequencing platforms, and generated from three different environmental sources. By designing and developing a flexible and customized pipeline, this study has showed how to process large metagenomic data sets with limited resources. This result not only would help to uncover new information from environmental samples, but also, could be applicable to any other metagenomic studies across various disciplines.

bioinformatics↗
bioRxiv2020

Uncovering the Structure and Function of Microbial Communities Formed During Periodic Tilling of TNT and DNT Co-Contaminated Soils

1.Environmental contamination by 2,4,6-trinitrotoluene (TNT), historically the most widely used secondary explosive, is a long-standing problem in former military conflict areas and at manufacturing and decommissioning plants. In field test plots at a former explosives manufacturing site, removal of TNT and dinitrotoluenes (DNTs) was observed following periods of tillage. Since tilling of soils has previously been shown to alter the microbial community, this study was aimed at understanding how the microbial community is altered in soils with historical contamination of nitro explosives from the former Barksdale TNT plant. Samples of untilled pristine soils, untilled TNT-contaminated soils and tilled TNT-contaminated soils were subjected to targeted amplicon sequencing of 16S ribosomal RNA genes in order to compare the structure of their bacterial communities. In addition, metagenomic data generated from the TNT tilled soil was used to understand the potential functions of the bacterial community relevant to nitroaromatic degradation. While the biodiversity dropped and the Burkholderiales order became dominant in both tilled and untilled soil regardless of tillage, the bacterial community composition at finer taxonomic levels revealed a greater difference between the two treatments. Functional analysis of metagenome assembled genome (MAG) bins through systematic review of commonly proposed DNT and TNT biotransformation pathways suggested that both aerobic and anaerobic degradation pathways were present. A proposed pathway that considers both aerobic and anaerobic steps in the degradation of TNT in the scenario of the tilled contaminated soils is presented. 2. ImportanceIn this study, TNT and DNT removal has been observed in field-scale experiments following periodic tilling of historically contaminated soils. The microbial community structures of uncontaminated pristine soils, untilled contaminated soils, and tilled contaminated soils were investigated using high-throughput sequencing platforms. In addition, shotgun metagenome libraries of samples from tilled contaminated soils were generated. The results indicated that a significant shift of the bacterial community at the family level between tilled and untilled contaminated soils, with tilled soils being dominated by Alcaligenaceae and untilled soils by Burkholderiacea. In-depth metagenomic analysis of samples from tilled contaminated soils, indicate the presence of genes that encode for enzymes that potentially could lead to mineralization of TNT and DNT under mixed aerobic and anaerobic periods.

genomics↗