Publications by authors named "J Alhama"

29 Publications

Meta-omic evaluation of bacterial microbial community structure and activity for the environmental assessment of soils: overcoming protein extraction pitfalls.

Environ Microbiol 2021 Jul 13. Epub 2021 Jul 13.

Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain.

Microorganisms play unique, essential and integral roles in the biosphere. This work aims to assess the utility of soil's metaomics for environmental diagnosis. Doñana National Park (DNP) was selected as a natural lab since it contains a strictly protected core that is surrounded by numerous threats of pollution. Culture-independent high-throughput molecular tools were used to evaluate the alterations of the global structure and metabolic activities of the microbiome. 16S rRNA sequencing shows lower bacterial abundance and diversity in areas historically exposed to contamination that surround DNP. For metaproteomics, an innovative post-alkaline protein extraction protocol was developed. After NaOH treatment, successive washing with Tris-HCl buffer supplemented with glycerol was essential to eliminate interferences. Starting from soils with different physicochemical characteristics, the method renders proteins with a remarkable resolution on SDS-PAGE gels. The proteins extracted were analysed by using an in-house database constructed from the rRNA data. LC-MS/MS analysis identified 2182 non-redundant proteins with 135 showing significant differences in relative abundance in the soils around DNP. Relevant global biological processes were altered in response to the environmental changes, such as protective and antioxidant mechanisms, translation, folding and homeostasis of proteins, membrane transport and aerobic respiratory metabolism.
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http://dx.doi.org/10.1111/1462-2920.15673DOI Listing
July 2021

Influence of packing material on the biofiltration of butyric acid: A comparative study from a physico-chemical, olfactometric and microbiological perspective.

J Environ Manage 2021 Sep 12;294:113044. Epub 2021 Jun 12.

Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Universidad de Córdoba, Campus Universitario de Rabanales, Carretera N-IV, Km 396, Edificio Marie Curie, 14071, Córdoba, Spain. Electronic address:

The influence of bed material on the odor removal performance of a biofilter was studied. A compost-wood biofilter and a wood biofilter were treated with a gaseous stream contaminated with butyric acid and comparatively evaluated at pilot scale using olfactometric, physico-chemical and microbiological approaches. The variables analyzed in both biofilters were correlated with specific families of their microbiota composition. In addition to a higher nutrients content (nitrogen and phosphorus), the compost-wood biofilter registered maximum values in number of aerobic microorganisms (3.6·10 CFU/g) and in aerobic microbiological activity (≈40 mg O/g VS of cumulative oxygen demand at 20 h). This may explain the higher performance of this biofilter compared to the wood biofilter, withstanding odor loads of up to 1450 ou/m·s with odor removal efficiencies close to 100%. The analysis of the microbial community showed that Actinobacteria, particularly the mostly aerobic Microbacteriaceae family, might play an important role in butyric acid degradation and hence reduce odor impact. The multidisciplinary analysis carried out in this work could be a very useful strategy for the optimal design of biofiltration operations.
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http://dx.doi.org/10.1016/j.jenvman.2021.113044DOI Listing
September 2021

Constructing a de novo transcriptome and a reference proteome for the bivalve Scrobicularia plana: Comparative analysis of different assembly strategies and proteomic analysis.

Genomics 2021 May 25;113(3):1543-1553. Epub 2021 Mar 25.

Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain. Electronic address:

Scrobicularia plana is a coastal and estuarine bivalve widely used in ecotoxicological studies. However, the underlying molecular mechanisms for S. plana pollutant responses are hardly known due to the lack of molecular databases. Thus, in this study we present a holistic approach to assess a robust reference transcriptome and proteome of this clam. A mixture of control and metal-exposed individuals was used for mRNA isolation. Four sets of high quality filtered preprocessed reads were generated (two quality scores and two sequenced lengths) and assembled with Mira, Ray and Trinity algorithms. The sixty-four generated assemblies were refined, filtered and evaluated for their proteomic quality. Eight assemblies presented top Detonate scores but one was selected due to its compactness and biological representation, which was generated: (i) from the highest quality dataset (Q20L100), (ii) using Trinity algorithm with all k-mers (AtKa), (iii) removing redundancy by CD-HIT (RR80), and (iv) filtering out poor contigs (F), that was subsequently named Q20L100AtKaRR80F. S. plana proteomic analysis revealed 10,017 peptide groups that corresponded to 2066 proteins with a wide coverage of molecular functions and biological processes, confirming the strength of the database generated.
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http://dx.doi.org/10.1016/j.ygeno.2021.03.025DOI Listing
May 2021

High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments.

Microb Biotechnol 2021 05 9;14(3):870-885. Epub 2021 Feb 9.

Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain.

Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.
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http://dx.doi.org/10.1111/1751-7915.13763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085945PMC
May 2021

Biofiltration of butyric acid: Monitoring odor abatement and microbial communities.

Environ Res 2020 11 14;190:110057. Epub 2020 Aug 14.

Chemical Engineering Department, University of Cordoba, Campus Universitario de Rabanales, Ctra. N-IV, Km 396, Building Marie Curie (C-3), 14071, Córdoba, Spain. Electronic address:

The objective of this study is to evaluate comparatively the odor removal efficacy of two biofilters operated under different conditions and to identify taxonomically the microbial communities responsible for butyric acid degradation. Both biofiltration systems, which were filled with non-inoculated wood chips and exposed to gas streams containing butyric acid, were evaluated under different operational conditions (gas airflow and temperature) from the physical-chemical, microbiological and olfactometric points of view. The physical-chemical characterization showed the acidification of the packing material and the accumulation of butyric acid during the biofiltration process (<60 days). The removal efficacy was found to be 98-100% during the first 20 days of operation, even at high odor concentration. Changes in the operational temperature increased the odor load factor from 400 to 1400 ou/m·s, which led to the reduction of microbiota in the packing material, and a drastic drop of the odor removal efficacy. However, the progressive increase in gas airflow improved the biodegradation efficacy of butyric acid up to 88% with odor loadings as high as 33,000 ou/m, while a linear relationship between odor inlet load and removal capacity was also found. The analysis of the microbial community showed that Proteobacteria was the most abundant phylum along the biofiltration time (58-92%) and regardless of the operational conditions. Finally, principal component analysis applied to the physical-chemical and microbiological data set revealed significant differences between the two biofilters under study.
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http://dx.doi.org/10.1016/j.envres.2020.110057DOI Listing
November 2020
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