26 results on '"Guerrero, Leandro"'
Search Results
2. Extracellular hydrolytic potential drives microbiome shifts during anaerobic co-digestion of sewage sludge and food waste
- Author
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Orellana, Esteban, Guerrero, Leandro D., Davies-Sala, Carol, Altina, Melisa, Pontiggia, Rodrigo M., and Erijman, Leonardo
- Published
- 2022
- Full Text
- View/download PDF
3. Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system
- Author
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Guerrero, Leandro D., Pérez, María V., Orellana, Esteban, Piuri, Mariana, Quiroga, Cecilia, and Erijman, Leonardo
- Published
- 2021
- Full Text
- View/download PDF
4. Tartrate fermentation with H2 production by a new member of Sporomusaceae enriched from rice paddy soil.
- Author
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Pereira-Mora, Luciana, Guerrero, Leandro D., Erijman, Leonardo, and Fernández-Scavino, Ana
- Subjects
- *
PLANT exudates , *METHANOGENS , *FERMENTATION , *PADDY fields , *DICARBOXYLIC acids , *SOILS - Abstract
In rice paddies, soil and plant-derived organic matter are degraded anaerobically to methane (CH4), a powerful greenhouse gas. The highest rate of methane emission occurs during the reproductive stage of the plant when mostly dicarboxylic acids are exudated by the roots. The emission of methane at this stage depends largely on the cooperative interaction between dicarboxylic acid-fermenting bacteria and methanogenic archaea in the rhizosphere. The fermentation of tartrate, one of the major acids exudated, has been scarcely explored in rice paddy soils. In this work, we characterized an anaerobic consortium from rice paddy soil composed of four bacterial strains, whose principal member (LT8) can ferment tartrate, producing H2 and acetate. Tartrate fermentation was accelerated by co-inoculation with a hydrogenotrophic methanogen. The assembled genome of LT8 possesses a Na+-dependent oxaloacetate decarboxylase and shows that this bacterium likely invests part of the H2 produced to reduce NAD(P)+ to assimilate C from tartrate. The phylogenetic analysis of the 16S rRNA gene, the genome-based classification as well as the average amino acid identity (AAI) indicated that LT8 belongs to a new genus within the Sporomusaceae family. LT8 shares a few common features with its closest relatives, for which tartrate degradation has not been described. LT8 is limited to a few environments but is more common in rice paddy soils, where it might contribute to methane emissions from root exudates. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
5. Evidence of microbial rhodopsins in Antarctic Dry Valley edaphic systems
- Author
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Guerrero, Leandro D., Vikram, Surendra, Makhalanyane, Thulani P., and Cowan, Don A.
- Published
- 2017
- Full Text
- View/download PDF
6. Nonrandom Assembly of Bacterial Populations in Activated Sludge Flocs
- Author
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Ayarza, Joaquín M., Guerrero, Leandro D., and Erijman, Leonardo
- Published
- 2010
7. Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale
- Author
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Figuerola, Eva L. M., Guerrero, Leandro D., Türkowsky, Dominique, Wall, Luis G., and Erijman, Leonardo
- Published
- 2015
- Full Text
- View/download PDF
8. Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia
- Author
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Ferrero Marcela A, Di Marzio Walter D, Guerrero Leandro D, Riva Mercadal Juan P, Lozada Mariana, and Dionisi Hebe M
- Subjects
Microbiology ,QR1-502 - Abstract
Abstract Background Polycyclic aromatic hydrocarbons (PAHs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. Our knowledge of PAH-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. In this work, genes coding catabolic enzymes from PAH-biodegradation pathways were characterized in coastal sediments of Patagonia with different levels of PAH contamination. Results Genes encoding for the catalytic alpha subunit of aromatic ring-hydroxylating dioxygenases (ARHDs) were amplified from intertidal sediment samples using two different primer sets. Products were cloned and screened by restriction fragment length polymorphism analysis. Clones representing each restriction pattern were selected in each library for sequencing. A total of 500 clones were screened in 9 gene libraries, and 193 clones were sequenced. Libraries contained one to five different ARHD gene types, and this number was correlated with the number of PAHs found in the samples above the quantification limit (r = 0.834, p < 0.05). Overall, eight different ARHD gene types were detected in the sediments. In five of them, their deduced amino acid sequences formed deeply rooted branches with previously described ARHD peptide sequences, exhibiting less than 70% identity to them. They contain consensus sequences of the Rieske type [2Fe-2S] cluster binding site, suggesting that these gene fragments encode for ARHDs. On the other hand, three gene types were closely related to previously described ARHDs: archetypical nahAc-like genes, phnAc-like genes as identified in Alcaligenes faecalis AFK2, and phnA1-like genes from marine PAH-degraders from the genus Cycloclasticus. Conclusion These results show the presence of hitherto unidentified ARHD genes in this sub-Antarctic marine environment exposed to anthropogenic contamination. This information can be used to study the geographical distribution and ecological significance of bacterial populations carrying these genes, and to design molecular assays to monitor the progress and effectiveness of remediation technologies.
- Published
- 2008
- Full Text
- View/download PDF
9. Evidence of microbial rhodopsins in Antarctic Dry Valley edaphic systems
- Author
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Guerrero, Leandro Demián, Vikram, Surendra, Makhalanyane, Thulani P., and Cowan, Don A.
- Subjects
ANTARCTICA ,SOIL ,Ciencias Biológicas ,METAGENIMICS ,RHODOPSINS ,Otras Ciencias Biológicas ,CIENCIAS NATURALES Y EXACTAS - Abstract
Microorganisms able to synthesize rhodopsins have the capacity to translocate ions through their membranes, using solar energy to generate a proton motive force. Rhodopsins are the most abundant phototrophic proteins in oceanic surface waters and are key constituents in marine bacterial ecology. However, it remains unclear how rhodopsins are used in most microorganisms. Despite their abundance in marine and fresh-water systems, the presence of functional rhodopsin systems in edaphic habitats has never been reported. Here, we show the presence of several new putative H+, Na+ and Cl+ pumping rhodopsins identified by metagenomic analysis of Antarctic desert hypolithic communities. Reconstruction of two Proteobacteria genomes harboring xanthorhodopsin-like proteins and one Bacteroidetes genome with a Na-pumping-like rhodopsin indicated that these bacteria were aerobic heterotrophs possessing the apparent capacity for the functional expression of rhodopsins. The existence of these protein systems in hypolithic bacteria expands the known role of rhodopsins to include terrestrial environments and suggests a possible predominant function as heterotrophic energy supply proteins, a feasible microbial adaptation to the harsh conditions prevalent in Antarctic edaphic systems. Fil: Guerrero, Leandro Demián. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. University of Pretoria. Department of Genetics. Centre of Microbial Ecology and Genomics; Sudáfrica Fil: Vikram, Surendra. University of Pretoria. Department of Genetics. Centre of Microbial Ecology and Genomics; Sudáfrica Fil: Makhalanyane, Thulani P.. University of Pretoria. Department of Genetics. Centre of Microbial Ecology and Genomics; Sudáfrica Fil: Cowan, Don A.. University of Pretoria. Department of Genetics. Centre of Microbial Ecology and Genomics; Sudáfrica
- Published
- 2017
10. Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community
- Author
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Vikram, Surendra, Guerrero, Leandro Demián, Makhalanyane, Thulani P., Le, Phuong T., Seely, Mary, and Cowan, Don A.
- Subjects
Ciencias Biológicas ,Hypoliths ,Otras Ciencias Biológicas ,Environmental Microbiology ,Metagenomics ,Desert ,CIENCIAS NATURALES Y EXACTAS - Abstract
In hyperarid ecosystems, macroscopic communities are often restricted to cryptic niches, such as hypoliths (microbial communities found beneath translucent rocks), which are widely distributed in hyperarid desert environments. While hypolithic communities are considered to play a major role in productivity, the functional guilds implicated in these processes remain unclear. Here, we describe the metagenomic sequencing, assembly and analysis of hypolithic microbial communities from the Namib Desert. Taxonomic analyses using Small Subunit phylogenetic markers showed that bacterial phylotypes (93%) dominated the communities, with relatively small proportions of archaea (0.43%) and fungi (5.6%). Refseq-viral database analysis showed the presence of double stranded DNA viruses (7.8% contigs), dominated by Caudovirales (59.2%). Analysis of functional genes and metabolic pathways revealed that cyanobacteria were primarily responsible for photosynthesis with the presence of multiple copies of genes for both photosystems I and II, with a smaller but significant fraction of proteobacterial anoxic photosystem II genes. Hypolithons demonstrated an extensive genetic capacity for the degradation of phosphonates and mineralization of organic sulphur. Surprisingly, we were unable to show the presence of genes representative of complete nitrogen cycles. Taken together, our analyses suggest an extensive capacity for carbon, phosphate and sulphate cycling but only limited nitrogen biogeochemistry. Fil: Vikram, Surendra. University of Pretoria; Sudáfrica Fil: Guerrero, Leandro Demián. University of Pretoria; Sudáfrica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina Fil: Makhalanyane, Thulani P.. University of Pretoria; Sudáfrica Fil: Le, Phuong T.. University of Pretoria; Sudáfrica Fil: Seely, Mary. Gobabeb Research and Training Centr; Namibia Fil: Cowan, Don A.. University of Pretoria; Sudáfrica
- Published
- 2016
11. Microbiome network analysis of co-occurrence patterns in anaerobic co-digestion of sewage sludge and food waste.
- Author
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Orellana, Esteban, Davies-Sala, Carol, Guerrero, Leandro D., Vardé, Ignacio, Altina, Melisa, Lorenzo, María Cielo, Figuerola, Eva L., Pontiggia, Rodrigo M., and Erijman, Leonardo
- Subjects
ORGANIC wastes ,SEWAGE sludge ,SEWAGE disposal plants ,METHANOGENS ,MICROBIAL communities ,LANDFILLS - Abstract
Addition of food waste (FW) as a co-substrate in anaerobic digesters of wastewater treatment plants is a desirable strategy towards achievement of the potential of wastewater treatment plants to become energy-neutral, diverting at the same time organic waste from landfills. Because substrate type is a driver of variations in phylogenetic structure of digester microbiomes, it is critical to understand how microbial communities respond to changes in substrate composition and concentration. In this work, high throughput sequencing was used to monitor the dynamics of microbiome changes in four parallel laboratory-scale anaerobic digesters treating sewage sludge during acclimation to an increasing amount of food waste. A co-occurrence network was constructed using data from 49 metagenomes sampled over the 161 days of the digesters' operation. More than half of the nodes in the network were clustered in two major modules, i.e. groups of highly interconnected taxa that had much fewer connections with taxa outside the group. The dynamics of co-occurrence networks evidenced shifts that occurred within microbial communities due to the addition of food waste in the co-digestion process. A diverse and reproducible group of hydrolytic and fermentative bacteria, syntrophic bacteria and methanogenic archaea appeared to grow in a concerted fashion to allow stable performance of anaerobic co-digestion at high FW. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
12. Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale
- Author
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Figuerola, Eva Lucia Margarita, Guerrero, Leandro Demián, Türkovsky, Dominique, Wall, Luis Gabriel, and Erijman, Leonardo
- Subjects
Ciencias Biológicas ,Bacteria ,Microbial Communities ,CIENCIAS AGRÍCOLAS ,Environmental signals ,Agricultura, Silvicultura y Pesca ,Ciencias del Suelo ,CIENCIAS NATURALES Y EXACTAS ,Microbial Ecology ,Conservación de la Biodiversidad - Abstract
The goal of this study was to investigate the spatial turnover of soil bacterial communities in response to environmental changes introduced by the practices of soybean monoculture or crop rotations, relative to grassland soils. Amplicon sequencing of the 16S rRNA gene was used to analyze bacterial diversity in producer fields through three successive cropping cycles within one and a half years, across a regional scale of 400 km at the Argentinean Pampas. Unlike local diversity, which was not significantly affected by land use type, agricultural management had a strong influence on β-diversity patterns. Distributions of pairwise distances between all soils samples under soybean monoculture had significantly lower β-diversity and narrower breadth compared to distributions of pairwise distances between soils managed with crop rotation. Interestingly, good agricultural practices had similar degree of β-diversity as natural grasslands. The higher phylogenetic relatedness of bacterial communities in soils under monoculture across the region were likely determined by the observed loss of endemic species, and affected mostly to phyla with low regional diversity, such as Acidobacteria, Verrucomicrobia and the candidates phyla SPAM and WS3. These results suggest that the implementation of good agricultural practices, including crop rotation, may be critical for the long-term conservation of soil biodiversity. Fil: Figuerola, Eva Lucia Margarita. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular; Argentina Fil: Guerrero, Leandro Demián. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular; Argentina Fil: Türkovsky, Dominique. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular; Argentina Fil: Wall, Luis Gabriel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnologia; Argentina Fil: Erijman, Leonardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina
- Published
- 2014
13. Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypolithsfrom Extreme Hyperarid Deserts.
- Author
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Phuong Thi Le, Makhalanyane, Thulani P., Guerrero, Leandro D., Vikram, Surendra, Van de Peer, Yves, and Cowan, Don A.
- Subjects
MICROBIOLOGY ,BIODIVERSITY ,ADAPTIVE radiation ,AMINO acids ,NUCLEOTIDE metabolism ,ADENOSINE triphosphate metabolism - Abstract
Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
14. Draft genomic DNA sequence of the multi-resistant Sphingomonas sp. strain AntH11 isolated from an Antarctic hypolith.
- Author
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Gunnigle, Eoin, Ramond, Jean-Baptiste, Guerrero, Leandro D., Makhalanyane, Thulani P., and Cowan, Don A.
- Subjects
NUCLEOTIDE sequencing ,SPHINGOMONAS ,BACTERIAL communities - Abstract
Hypoliths are microbial communities that live underneath translucent rocks in desert ecosystems and represent a key refuge niche in the Antarctic Dry Valleys. These cryptic microbial assemblages are crucial as they mediate numerous ecosystem processes. Here, we present the first draft genome of a hypolith isolate belonging to the α-proteobacterial class and the genus Sphingomonas. The draft genome of Sphingomonas sp. strain AntH11 shows the capacity of this organism to adapt to the extreme cold and arid conditions encountered in Antarctic desert soils. Our result also suggests that its metabolic versatility and multidrug resistance constitutes an opportunistic advantage in competition with other hypolith-colonizing microorganisms. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
15. Bacterial Indicator of Agricultural Management for Soil under No-Till Crop Production.
- Author
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Figuerola, Eva L. M., Guerrero, Leandro D., Rosa, Silvina M., Simonetti, Leandro, Duval, Matías E., Galantini, Juan A., Bedano, Josí C., Wall, Luis G., and Erijman, Leonardo
- Subjects
- *
SOIL fertility research , *FOOD industry , *FUNGUS-bacterium relationships , *SOIL productivity , *CROP rotation , *AGRICULTURAL productivity - Abstract
The rise in the world demand for food poses a challenge to our ability to sustain soil fertility and sustainability. The increasing use of no-till agriculture, adopted in many areas of the world as an alternative to conventional farming, may contribute to reduce the erosion of soils and the increase in the soil carbon pool. However, the advantages of no-till agriculture are jeopardized when its use is linked to the expansion of crop monoculture. The aim of this study was to survey bacterial communities to find indicators of soil quality related to contrasting agriculture management in soils under no-till farming. Four sites in production agriculture, with different soil properties, situated across a west-east transect in the most productive region in the Argentinean pampas, were taken as the basis for replication. Working definitions of Good no-till Agricultural Practices (GAP) and Poor no-till Agricultural Practices (PAP) were adopted for two distinct scenarios in terms of crop rotation, fertilization, agrochemicals use and pest control. Non-cultivated soils nearby the agricultural sites were taken as additional control treatments. Tag-encoded pyrosequencing was used to deeply sample the 16S rRNA gene from bacteria residing in soils corresponding to the three treatments at the four locations. Although bacterial communities as a whole appeared to be structured chiefly by a marked biogeographic provincialism, the distribution of a few taxa was shaped as well by environmental conditions related to agricultural management practices. A statistically supported approach was used to define candidates for management-indicator organisms, subsequently validated using quantitative PCR. We suggest that the ratio between the normalized abundance of a selected group of bacteria within the GP1 group of the phylum Acidobacteria and the genus Rubellimicrobium of the Alphaproteobacteria may serve as a potential management-indicator to discriminate between sustainable vs. non-sustainable agricultural practices in the Pampa region. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
16. Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia.
- Author
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Lozada, Mariana, Riva Mercadal, Juan P., Guerrero, Leandro D., Di Marzio, Walter D., Ferrero, Marcela A., and Dionisi, Hebe M.
- Subjects
POLYCYCLIC aromatic hydrocarbons ,MARINE sediments ,MARINE organisms ,COASTAL sediments ,ALCALIGENES - Abstract
Background: Polycyclic aromatic hydrocarbons (PAHs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. Our knowledge of PAH-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. In this work, genes coding catabolic enzymes from PAH-biodegradation pathways were characterized in coastal sediments of Patagonia with different levels of PAH contamination. Results: Genes encoding for the catalytic alpha subunit of aromatic ring-hydroxylating dioxygenases (ARHDs) were amplified from intertidal sediment samples using two different primer sets. Products were cloned and screened by restriction fragment length polymorphism analysis. Clones representing each restriction pattern were selected in each library for sequencing. A total of 500 clones were screened in 9 gene libraries, and 193 clones were sequenced. Libraries contained one to five different ARHD gene types, and this number was correlated with the number of PAHs found in the samples above the quantification limit (r = 0.834, p < 0.05). Overall, eight different ARHD gene types were detected in the sediments. In five of them, their deduced amino acid sequences formed deeply rooted branches with previously described ARHD peptide sequences, exhibiting less than 70% identity to them. They contain consensus sequences of the Rieske type [2Fe-2S] cluster binding site, suggesting that these gene fragments encode for ARHDs. On the other hand, three gene types were closely related to previously described ARHDs: archetypical nahAc-like genes, phnAc-like genes as identified in Alcaligenes faecalis AFK2, and phnA1-like genes from marine PAH-degraders from the genus Cycloclasticus. Conclusion: These results show the presence of hitherto unidentified ARHD genes in this sub-Antarctic marine environment exposed to anthropogenic contamination. This information can be used to study the geographical distribution and ecological significance of bacterial populations carrying these genes, and to design molecular assays to monitor the progress and effectiveness of remediation technologies. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
17. Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil.
- Author
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Gunnigle, Eoin, Frossard, Aline, Ramond, Jean-Baptiste, Guerrero, Leandro, Seely, Mary, and Cowan, Don A.
- Abstract
Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were 'time-of-day-dependent' which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module 'hubs' orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
18. The influence of soil properties on denitrifying bacterial communities and denitrification potential in no-till production farms under contrasting management in the Argentinean Pampas.
- Author
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Rosa, Silvina M., Behrends Kraemer, Filipe, Soria, Marcelo A., Guerrero, Leandro D., Morrás, Héctor J.M., Figuerola, Eva L.M., and Erijman, Leonardo
- Subjects
- *
DENITRIFICATION , *BACTERIAL population , *SOIL microbiology , *SOIL management , *STRUCTURAL stability - Abstract
Highlights: [•] Variance components analysis discriminated dynamic and inherent soil properties. [•] Inherent soil properties modified denitrifying abundance and potential activity. [•] Most dynamic soil properties were site-specific. [•] Potential denitrification was associated to indexes of structural stability. [Copyright &y& Elsevier]
- Published
- 2014
- Full Text
- View/download PDF
19. Tartrate fermentation with H 2 production by a new member of Sporomusaceae enriched from rice paddy soil.
- Author
-
Pereira-Mora L, Guerrero LD, Erijman L, and Fernández-Scavino A
- Subjects
- Soil chemistry, Fermentation, Tartrates metabolism, RNA, Ribosomal, 16S genetics, RNA, Ribosomal, 16S metabolism, Phylogeny, Base Composition, Sequence Analysis, DNA, Bacteria, Bacteria, Anaerobic metabolism, Firmicutes metabolism, Gram-Negative Bacteria genetics, Methane metabolism, Oryza microbiology, Euryarchaeota metabolism
- Abstract
In rice paddies, soil and plant-derived organic matter are degraded anaerobically to methane (CH
4 ), a powerful greenhouse gas. The highest rate of methane emission occurs during the reproductive stage of the plant when mostly dicarboxylic acids are exudated by the roots. The emission of methane at this stage depends largely on the cooperative interaction between dicarboxylic acid-fermenting bacteria and methanogenic archaea in the rhizosphere. The fermentation of tartrate, one of the major acids exudated, has been scarcely explored in rice paddy soils. In this work, we characterized an anaerobic consortium from rice paddy soil composed of four bacterial strains, whose principal member (LT8) can ferment tartrate, producing H2 and acetate. Tartrate fermentation was accelerated by co-inoculation with a hydrogenotrophic methanogen. The assembled genome of LT8 possesses a Na+ -dependent oxaloacetate decarboxylase and shows that this bacterium likely invests part of the H2 produced to reduce NAD(P)+ to assimilate C from tartrate. The phylogenetic analysis of the 16S rRNA gene, the genome-based classification as well as the average amino acid identity (AAI) indicated that LT8 belongs to a new genus within the Sporomusaceae family. LT8 shares a few common features with its closest relatives, for which tartrate degradation has not been described. LT8 is limited to a few environments but is more common in rice paddy soils, where it might contribute to methane emissions from root exudates.IMPORTANCEThis is the first report of the metabolic characterization of a new anaerobic bacterium able to degrade tartrate, a compound frequently associated with plants, but rare as a microbial metabolite. Tartrate fermentation by this bacterium can be coupled to methanogenesis in the rice rhizosphere where tartrate is mainly produced at the reproductive stage of the plant, when the maximum methane rate emission occurs. The interaction between secondary fermentative bacteria, such as LT8, and methanogens could represent a fundamental step in exploring mitigation strategies for methane emissions from rice fields. Possible strategies could include controlling the activity of these secondary fermentative bacteria or selecting plants whose exudates are more difficult to ferment., Competing Interests: The authors declare no conflict of interest.- Published
- 2024
- Full Text
- View/download PDF
20. Time Series Genome-Centric Analysis Unveils Bacterial Response to Operational Disturbance in Activated Sludge.
- Author
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Pérez MV, Guerrero LD, Orellana E, Figuerola EL, and Erijman L
- Abstract
Understanding ecosystem response to disturbances and identifying the most critical traits for the maintenance of ecosystem functioning are important goals for microbial community ecology. In this study, we used 16S rRNA amplicon sequencing and metagenomics to investigate the assembly of bacterial populations in a full-scale municipal activated sludge wastewater treatment plant over a period of 3 years, including a 9-month period of disturbance characterized by short-term plant shutdowns. Following the reconstruction of 173 metagenome-assembled genomes, we assessed the functional potential, the number of rRNA gene operons, and the in situ growth rate of microorganisms present throughout the time series. Operational disturbances caused a significant decrease in bacteria with a single copy of the rRNA ( rrn ) operon. Despite moderate differences in resource availability, replication rates were distributed uniformly throughout time, with no differences between disturbed and stable periods. We suggest that the length of the growth lag phase, rather than the growth rate, is the primary driver of selection under disturbed conditions. Thus, the system could maintain its function in the face of disturbance by recruiting bacteria with the capacity to rapidly resume growth under unsteady operating conditions. IMPORTANCE Disturbance is a key determinant of community assembly and dynamics in natural and engineered ecosystems. Microbiome response to disturbance is thought to be influenced by bacterial growth traits and life history strategies. In this time series observational study, the response to disturbance of microbial communities in a full-scale activated sludge wastewater treatment plant was assessed by computing specific cellular traits of genomes retrieved from metagenomes. It was found that the genomes observed in disturbed periods have more copies of the rRNA operon than genomes observed in stable periods, whereas the in situ mean relative growth rates of bacteria present during stable and disturbed periods were indistinguishable. From these intriguing observations, we infer that the length of the lag phase might be a growth trait that affects the microbial response to disturbance. Further exploration of this hypothesis could contribute to better understanding of the adaptive response of microbiomes to unsteady environmental conditions., (Copyright © 2019 Pérez et al.)
- Published
- 2019
- Full Text
- View/download PDF
21. Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts.
- Author
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Le PT, Makhalanyane TP, Guerrero LD, Vikram S, Van de Peer Y, and Cowan DA
- Subjects
- Actinobacteria genetics, Actinobacteria isolation & purification, Antarctic Regions, Bacteroidetes genetics, Bacteroidetes isolation & purification, Cyanobacteria genetics, Cyanobacteria isolation & purification, Desert Climate, Proteobacteria genetics, Proteobacteria isolation & purification, Extreme Environments, Metagenome, Microbiota, Stress, Physiological
- Abstract
Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes., (© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2016
- Full Text
- View/download PDF
22. Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community.
- Author
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Vikram S, Guerrero LD, Makhalanyane TP, Le PT, Seely M, and Cowan DA
- Subjects
- Archaea classification, Archaea genetics, Bacteria classification, Bacteria isolation & purification, Carbon metabolism, Desert Climate, Ecosystem, Fungi classification, Fungi genetics, Metagenomics, Phylogeny, Soil chemistry, Archaea isolation & purification, Bacteria genetics, Fungi isolation & purification, Soil Microbiology
- Abstract
In hyperarid ecosystems, macroscopic communities are often restricted to cryptic niches, such as hypoliths (microbial communities found beneath translucent rocks), which are widely distributed in hyperarid desert environments. While hypolithic communities are considered to play a major role in productivity, the functional guilds implicated in these processes remain unclear. Here, we describe the metagenomic sequencing, assembly and analysis of hypolithic microbial communities from the Namib Desert. Taxonomic analyses using Small Subunit phylogenetic markers showed that bacterial phylotypes (93%) dominated the communities, with relatively small proportions of archaea (0.43%) and fungi (5.6%). Refseq-viral database analysis showed the presence of double stranded DNA viruses (7.8% contigs), dominated by Caudovirales (59.2%). Analysis of functional genes and metabolic pathways revealed that cyanobacteria were primarily responsible for photosynthesis with the presence of multiple copies of genes for both photosystems I and II, with a smaller but significant fraction of proteobacterial anoxic photosystem II genes. Hypolithons demonstrated an extensive genetic capacity for the degradation of phosphonates and mineralization of organic sulphur. Surprisingly, we were unable to show the presence of genes representative of complete nitrogen cycles. Taken together, our analyses suggest an extensive capacity for carbon, phosphate and sulphate cycling but only limited nitrogen biogeochemistry., (© 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2016
- Full Text
- View/download PDF
23. Draft Genome Sequence of Sphingomonas sp. Strain Ant20, Isolated from Oil-Contaminated Soil on Ross Island, Antarctica.
- Author
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Ronca S, Frossard A, Guerrero LD, Makhalanyane TP, Aislabie JM, and Cowan DA
- Abstract
Here, we present the draft genome of Sphingomonas sp. strain Ant20, isolated from oil-polluted soil near Scott Base, Ross Island, Antarctica. The genome of this aromatic hydrocarbon-degrading bacterium provides valuable information on the microbially mediated biodegradation of aromatic compounds in cold-climate systems., (Copyright © 2015 Ronca et al.)
- Published
- 2015
- Full Text
- View/download PDF
24. Draft Genome Sequence of Microbacterium sp. Strain CH12i, Isolated from Shallow Groundwater in Cape Hallett, Antarctica.
- Author
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Ferreras ER, De Maayer P, Makhalanyane TP, Guerrero LD, Aislabie JM, and Cowan DA
- Abstract
The Antarctic continent is largely covered by an expansive ice sheet, but it harbors diverse terrestrial and aquatic habitats in the coastal ice-free continental margins. Here we present the draft genome of Microbacterium sp. CH12i, which was isolated from hypersaline, alkaline, and nutrient-rich groundwater from Cape Hallett, northern Victoria Land, Antarctica., (Copyright © 2014 Ferreras et al.)
- Published
- 2014
- Full Text
- View/download PDF
25. Draft Genome Sequence of the Aromatic Hydrocarbon-Degrading Bacterium Sphingobium sp. Strain Ant17, Isolated from Antarctic Soil.
- Author
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Adriaenssens EM, Guerrero LD, Makhalanyane TP, Aislabie JM, and Cowan DA
- Abstract
Here, we present the draft genome sequence of Sphingobium sp. strain Ant17, an aromatic hydrocarbon-degrading bacterium that was isolated from Antarctic oil-contaminated soil. An analysis of this genome can lead to insights into the mechanisms of xenobiotic degradation processes at low temperatures and potentially aid in bioremediation applications.
- Published
- 2014
- Full Text
- View/download PDF
26. Draft Genome Sequence of Williamsia sp. Strain D3, Isolated From the Darwin Mountains, Antarctica.
- Author
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Guerrero LD, Makhalanyane TP, Aislabie JM, and Cowan DA
- Abstract
Actinobacteria are the dominant taxa in Antarctic desert soils. Here, we describe the first draft genome of a member of the genus Williamsia (strain D3) isolated from Antarctic soil. The genome of this psychrotolerant bacterium may help to elucidate crucial survival mechanisms for organisms inhabiting cold desert soil systems.
- Published
- 2014
- Full Text
- View/download PDF
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