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Michal Koblížek - One of the best experts on this subject based on the ideXlab platform.
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Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes.
Frontiers in microbiology, 2021Co-Authors: Yonghui Zeng, Nupur, Anne Mette Madsen, Xihan Chen, Alastair T. Gardiner, Michal KoblížekAbstract:The bacterial phylum Gemmatimonadetes contains members capable of performing bacteriochlorophyll-based phototrophy (chlorophototrophy). However, only one strain of chlorophototrophic Gemmatimonadetes bacteria (CGB) has been isolated to date, hampering our further understanding of their photoheterotrophic lifestyle and the evolution of phototrophy in CGB. By combining a culturomics strategy with a rapid screening technique for chlorophototrophs, we report the isolation of a new member of CGB, Gemmatimonas (G.) groenlandica sp. nov., from the surface water of a stream in the Zackenberg valley in High Arctic Greenland. Distinct from the microaerophilic G. phototrophica strain AP64T, G. groenlandica strain TET16T is a strictly aerobic anoxygenic phototroph, lacking many oxygen-independent enzymes while possessing an expanded arsenal for coping with oxidative stresses. Its pigment composition and infra-red absorption properties are also different from G. phototrophica, indicating that it possesses a different photosystem apparatus. The complete genome sequence of G. groenlandica reveals the unique and conserved features in the photosynthesis gene clusters of CGB. We further analyzed metagenome-assembled genomes of CGB obtained from soil and glacier metagenomes from northeast Greenland, revealing a wide distribution pattern of CGB beyond the stream water investigated. Originality/Importance The bacterial phylum Gemmatimonadetes is an important but yet understudied group in natural microbial communities. The isolation of the only phototrophic member of this phylum, Gemmatimonas phototrophica, was reported in 2014, which expanded the list of known bacterial phyla capable of performing photosynthesis. Since then, no new phototrophic member of this phylum has been isolated. By applying a novel isolation strategy of combining a mass spectroscopy-based high-throughput profiling method and a rapid screening technique for phototrophic bacterial colonies, we successfully isolated the second phototrophic member of this phylum, Gemmatimonas groenlandica, from a stream in Northeast Greenland. Its discovery confirms the widespread presence of phototrophic Gemmatimonadetes bacteria in the environment and raises an intriguing question on the evolutionary history of phototrophy in the phylum Gemmatimonadetes. Distinct from the microaerophilic slow growth rate evident with G. phototrophica, G. groenlandica is a strict aerobe and can be readily cultured in liquid medium, opening new possibilities for future strain genetic engineering and detailed photophysiological studies.
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Utilization of light energy in phototrophic Gemmatimonadetes.
Journal of photochemistry and photobiology. B Biology, 2020Co-Authors: Michal Koblížek, Marko Dachev, David Bína, Nupur, Kasia Piwosz, David KaftanAbstract:Abstract Gemmatimonas phototrophica is, so far, the only described phototrophic species of the bacterial phylum Gemmatimonadetes. Its cells contain a unique type of photosynthetic complex with the reaction center surrounded by a double ring antenna, however they can also grow in the dark using organic carbon substrates. Its photosynthesis genes were received via horizontal gene transfer from Proteobacteria. This raises two questions; how the horizontally transferred photosynthesis apparatus has integrated into the cellular machinery, and how much light-derived energy actually contributes to the cellular metabolism? To address these points, the photosynthetic reactions were studied on several levels, from photophysics of the reaction center to cellular growth. Flash photolysis measurements and bacteriochlorophyll fluorescence kinetic measurements documented the presence of fully functional type-2 reaction centers with a large light harvesting antenna. When illuminated, the bacterial cells reduced their respiration rate by 58 ± 5%, revealing that oxidative phosphorylation was replaced by photophosphorylation. Moreover, illumination also more than doubled the assimilation rates of glucose, a sugar that is mostly used for respiration. Finally, light increased the growth rates of Gemmatimonas phototrophica colonies on agar plates. All the presented data provide evidence that photosynthetic complexes are fully integrated into cellular metabolism of Gemmatimonas phototrophica, and are able to provide a substantial amount of energy for its metabolism and growth.
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Phototrophic Gemmatimonadetes – a New “Purple” Branch on the Bacterial Tree of Life
Modern Topics in the Phototrophic Prokaryotes, 2017Co-Authors: Yonghui Zeng, Michal KoblížekAbstract:Photosynthesis first emerged in prokaryotes over three billion years ago and represents one of the most fundamental biological processes on Earth. So far, species capable of performing (bacterio)chlorophyll-based phototrophy have been reported in seven bacterial phyla, i.e., Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Here we review the discovery, physiology, genomic characteristics, environmental distribution, and possible evolutionary origin of the bacterium Gemmatimonas phototrophica strain AP64, so far the only phototrophic member of the phylum Gemmatimonadetes. This organism was isolated from a freshwater lake in the Gobi Desert, North China in 2011. It contains fully functional type-2 photosynthetic reaction centers, but they seem to only serve as an auxiliary energy source. Its photosynthesis genes are located in a 42.3 kb long photosynthesis gene cluster which appear to originate from an ancient horizontal gene transfer from a purple phototrophic bacterium. A survey of biomarker genes of phototrophic Gemmatimonadetes bacteria (PGB) in public environmental genomics databases suggests that PGB are widely distributed in diverse environments, including air, river waters/sediment, estuarine waters, lake waters, biofilms, plant surfaces, intertidal sediments, soils, springs, and wastewater treatment plants, but none from marine waters or sediment. PGB make up roughly 0.4–11.9 % of whole phototrophic microbial communities in these habitats. The discovery of PGB presents a strong evidence that genes for anoxygenic phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.
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phototrophic Gemmatimonadetes a new purple branch on the bacterial tree of life
2017Co-Authors: Yonghui Zeng, Michal KoblížekAbstract:Photosynthesis first emerged in prokaryotes over three billion years ago and represents one of the most fundamental biological processes on Earth. So far, species capable of performing (bacterio)chlorophyll-based phototrophy have been reported in seven bacterial phyla, i.e., Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Here we review the discovery, physiology, genomic characteristics, environmental distribution, and possible evolutionary origin of the bacterium Gemmatimonas phototrophica strain AP64, so far the only phototrophic member of the phylum Gemmatimonadetes. This organism was isolated from a freshwater lake in the Gobi Desert, North China in 2011. It contains fully functional type-2 photosynthetic reaction centers, but they seem to only serve as an auxiliary energy source. Its photosynthesis genes are located in a 42.3 kb long photosynthesis gene cluster which appear to originate from an ancient horizontal gene transfer from a purple phototrophic bacterium. A survey of biomarker genes of phototrophic Gemmatimonadetes bacteria (PGB) in public environmental genomics databases suggests that PGB are widely distributed in diverse environments, including air, river waters/sediment, estuarine waters, lake waters, biofilms, plant surfaces, intertidal sediments, soils, springs, and wastewater treatment plants, but none from marine waters or sediment. PGB make up roughly 0.4–11.9 % of whole phototrophic microbial communities in these habitats. The discovery of PGB presents a strong evidence that genes for anoxygenic phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.
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Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica.
Public Library of Science (PLoS), 2017Co-Authors: Marko Dachev, David Bína, David Kaftan, Roman Sobotka, Lenka Moravcová, Zdenko Gardian, Václav Šlouf, Marcel Fuciman, Tomáš Polívka, Michal KoblížekAbstract:The majority of life on Earth depends directly or indirectly on the sun as a source of energy. The initial step of photosynthesis is facilitated by light-harvesting complexes, which capture and transfer light energy into the reaction centers (RCs). Here, we analyzed the organization of photosynthetic (PS) complexes in the bacterium G. phototrophica, which so far is the only phototrophic representative of the bacterial phylum Gemmatimonadetes. The isolated complex has a molecular weight of about 800 ± 100 kDa, which is approximately 2 times larger than the core complex of Rhodospirillum rubrum. The complex contains 62.4 ± 4.7 bacteriochlorophyll (BChl) a molecules absorbing in 2 distinct infrared absorption bands with maxima at 816 and 868 nm. Using femtosecond transient absorption spectroscopy, we determined the energy transfer time between these spectral bands as 2 ps. Single particle analyses of the purified complexes showed that they were circular structures with an outer diameter of approximately 18 nm and a thickness of 7 nm. Based on the obtained, we propose that the light-harvesting complexes in G. phototrophica form 2 concentric rings surrounding the type 2 RC. The inner ring (corresponding to the B868 absorption band) is composed of 15 subunits and is analogous to the inner light-harvesting complex 1 (LH1) in purple bacteria. The outer ring is composed of 15 more distant BChl dimers with no or slow energy transfer between them, resulting in the B816 absorption band. This completely unique and elegant organization offers good structural stability, as well as high efficiency of light harvesting. Our results reveal that while the PS apparatus of Gemmatimonadetes was acquired via horizontal gene transfer from purple bacteria, it later evolved along its own pathway, devising a new arrangement of its light harvesting complexes
Yonghui Zeng - One of the best experts on this subject based on the ideXlab platform.
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Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes.
Frontiers in microbiology, 2021Co-Authors: Yonghui Zeng, Nupur, Anne Mette Madsen, Xihan Chen, Alastair T. Gardiner, Michal KoblížekAbstract:The bacterial phylum Gemmatimonadetes contains members capable of performing bacteriochlorophyll-based phototrophy (chlorophototrophy). However, only one strain of chlorophototrophic Gemmatimonadetes bacteria (CGB) has been isolated to date, hampering our further understanding of their photoheterotrophic lifestyle and the evolution of phototrophy in CGB. By combining a culturomics strategy with a rapid screening technique for chlorophototrophs, we report the isolation of a new member of CGB, Gemmatimonas (G.) groenlandica sp. nov., from the surface water of a stream in the Zackenberg valley in High Arctic Greenland. Distinct from the microaerophilic G. phototrophica strain AP64T, G. groenlandica strain TET16T is a strictly aerobic anoxygenic phototroph, lacking many oxygen-independent enzymes while possessing an expanded arsenal for coping with oxidative stresses. Its pigment composition and infra-red absorption properties are also different from G. phototrophica, indicating that it possesses a different photosystem apparatus. The complete genome sequence of G. groenlandica reveals the unique and conserved features in the photosynthesis gene clusters of CGB. We further analyzed metagenome-assembled genomes of CGB obtained from soil and glacier metagenomes from northeast Greenland, revealing a wide distribution pattern of CGB beyond the stream water investigated. Originality/Importance The bacterial phylum Gemmatimonadetes is an important but yet understudied group in natural microbial communities. The isolation of the only phototrophic member of this phylum, Gemmatimonas phototrophica, was reported in 2014, which expanded the list of known bacterial phyla capable of performing photosynthesis. Since then, no new phototrophic member of this phylum has been isolated. By applying a novel isolation strategy of combining a mass spectroscopy-based high-throughput profiling method and a rapid screening technique for phototrophic bacterial colonies, we successfully isolated the second phototrophic member of this phylum, Gemmatimonas groenlandica, from a stream in Northeast Greenland. Its discovery confirms the widespread presence of phototrophic Gemmatimonadetes bacteria in the environment and raises an intriguing question on the evolutionary history of phototrophy in the phylum Gemmatimonadetes. Distinct from the microaerophilic slow growth rate evident with G. phototrophica, G. groenlandica is a strict aerobe and can be readily cultured in liquid medium, opening new possibilities for future strain genetic engineering and detailed photophysiological studies.
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Phototrophic Gemmatimonadetes – a New “Purple” Branch on the Bacterial Tree of Life
Modern Topics in the Phototrophic Prokaryotes, 2017Co-Authors: Yonghui Zeng, Michal KoblížekAbstract:Photosynthesis first emerged in prokaryotes over three billion years ago and represents one of the most fundamental biological processes on Earth. So far, species capable of performing (bacterio)chlorophyll-based phototrophy have been reported in seven bacterial phyla, i.e., Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Here we review the discovery, physiology, genomic characteristics, environmental distribution, and possible evolutionary origin of the bacterium Gemmatimonas phototrophica strain AP64, so far the only phototrophic member of the phylum Gemmatimonadetes. This organism was isolated from a freshwater lake in the Gobi Desert, North China in 2011. It contains fully functional type-2 photosynthetic reaction centers, but they seem to only serve as an auxiliary energy source. Its photosynthesis genes are located in a 42.3 kb long photosynthesis gene cluster which appear to originate from an ancient horizontal gene transfer from a purple phototrophic bacterium. A survey of biomarker genes of phototrophic Gemmatimonadetes bacteria (PGB) in public environmental genomics databases suggests that PGB are widely distributed in diverse environments, including air, river waters/sediment, estuarine waters, lake waters, biofilms, plant surfaces, intertidal sediments, soils, springs, and wastewater treatment plants, but none from marine waters or sediment. PGB make up roughly 0.4–11.9 % of whole phototrophic microbial communities in these habitats. The discovery of PGB presents a strong evidence that genes for anoxygenic phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.
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phototrophic Gemmatimonadetes a new purple branch on the bacterial tree of life
2017Co-Authors: Yonghui Zeng, Michal KoblížekAbstract:Photosynthesis first emerged in prokaryotes over three billion years ago and represents one of the most fundamental biological processes on Earth. So far, species capable of performing (bacterio)chlorophyll-based phototrophy have been reported in seven bacterial phyla, i.e., Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Here we review the discovery, physiology, genomic characteristics, environmental distribution, and possible evolutionary origin of the bacterium Gemmatimonas phototrophica strain AP64, so far the only phototrophic member of the phylum Gemmatimonadetes. This organism was isolated from a freshwater lake in the Gobi Desert, North China in 2011. It contains fully functional type-2 photosynthetic reaction centers, but they seem to only serve as an auxiliary energy source. Its photosynthesis genes are located in a 42.3 kb long photosynthesis gene cluster which appear to originate from an ancient horizontal gene transfer from a purple phototrophic bacterium. A survey of biomarker genes of phototrophic Gemmatimonadetes bacteria (PGB) in public environmental genomics databases suggests that PGB are widely distributed in diverse environments, including air, river waters/sediment, estuarine waters, lake waters, biofilms, plant surfaces, intertidal sediments, soils, springs, and wastewater treatment plants, but none from marine waters or sediment. PGB make up roughly 0.4–11.9 % of whole phototrophic microbial communities in these habitats. The discovery of PGB presents a strong evidence that genes for anoxygenic phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.
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Novel acsF Gene Primers Revealed a Diverse Phototrophic Bacterial Population, Including Gemmatimonadetes, in Lake Taihu (China).
Applied and environmental microbiology, 2016Co-Authors: Yili Huang, Yanhua Zeng, Hao Feng, Yonghui Zeng, Michal KoblížekAbstract:ABSTRACT Anoxygenic phototrophs represent an environmentally important and phylogenetically diverse group of organisms. They harvest light using bacteriochlorophyll-containing reaction centers. Recently, a novel phototrophic bacterium, Gemmatimonas phototrophica, belonging to a rarely studied phylum, Gemmatimonadetes, was isolated from a freshwater lake in the Gobi Desert. To obtain more information about the environmental distribution of phototrophic Gemmatimonadetes, we collected microbial samples from the water column, upper sediment, and deeper anoxic sediment of Lake Taihu, China. MiSeq sequencing of the 16S rRNA, pufM , and bchY genes was carried out to assess the diversity of local phototrophic communities. In addition, we designed new degenerate primers of aerobic cyclase gene acsF , which serves as a convenient marker for both phototrophic Gemmatimonadetes and phototrophic Proteobacteria. Our results showed that most of the phototrophic species in Lake Taihu belong to Alpha- and Betaproteobacteria. Sequences of green sulfur and green nonsulfur bacteria (phototrophic Chlorobi and Chloroflexi, respectively) were found in the sediment. Using the newly designed primers, we identified a diverse community of phototrophic Gemmatimonadetes forming 30 operational taxonomic units. These species represented 10.5 and 17.3% of the acsF reads in the upper semiaerobic sediment and anoxic sediment, whereas their abundance in the water column was IMPORTANCE Photosynthesis is one of the most fundamental biological processes on Earth. Recently, the presence of photosynthetic reaction centers has been reported from a rarely studied bacterial phylum, Gemmatimonadetes, but almost nothing is known about the diversity and environmental distribution of these organisms. The newly designed acsF primers were used to identify phototrophic Gemmatimonadetes from planktonic and sediment samples collected in Lake Taihu, China. The Gemmatimonadetes sequences were found mostly in the upper sediments, documenting the preference of Gemmatimonadetes for semiaerobic conditions. Our results also show that the phototrophic Gemmatimonadetes present in Lake Taihu were relatively diverse, encompassing 30 operational taxonomic units.
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Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments
Environmental microbiology reports, 2016Co-Authors: Yonghui Zeng, Jan Baumbach, Eudes Guilherme Vieira Barbosa, Vasco Azevedo, Chuanlun Zhang, Michal KoblížekAbstract:Gemmatimonadetes represents a poorly understood bacterial phylum with only a handful of cultured species. Recently, one of its few representatives, Gemmatimonas phototrophica, was found to contain purple bacterial photosynthetic reaction centres. However, almost nothing is known about the environmental distribution of phototrophic Gemmatimonadetes bacteria. To fill this gap, we took advantage of fast-growing public metagenomic databases and performed an extensive survey of metagenomes deposited into the NCBI's WGS database, the JGI's IMG webserver and the MG-RAST webserver. By employing Mg protoporphyrin IX monomethyl ester oxidative cyclase (AcsF) as a marker gene, we identified 291 AcsF fragments (24-361 amino acids long) that are closely related to G. phototrophica from 161 metagenomes originating from various habitats, including air, river waters/sediment, estuarine waters, lake waters, biofilms, plant surfaces, intertidal sediment, soils, springs and wastewater treatment plants, but none from marine waters or sediment. Based on AcsF hit counts, phototrophic Gemmatimonadetes bacteria make up 0.4-11.9% of whole phototrophic microbial communities in these habitats. Unexpectedly, an almost complete 37.9 kb long photosynthesis gene cluster with identical gene composition and arrangement to those in G. phototrophica was reconstructed from the Odense wastewater metagenome, only differing in a 7.2 kb long non-photosynthesis-gene insert. These data suggest that phototrophic Gemmatimonadetes bacteria are much more widely distributed in the environment and exhibit a higher genetic diversity than previously thought.
Luis M Sanchezrodriguez - One of the best experts on this subject based on the ideXlab platform.
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the bacterial community structure and microbial activity in a traditional organic milpa farming system under different soil moisture conditions
Frontiers in Microbiology, 2018Co-Authors: Ivan P Morenoespindola, Maria Jesus Ferraraguerrero, Marco Lunaguido, Daniel A Ramirezvillanueva, Arit S De Leonlorenzana, Selene Gomezacata, Elizabeth Gonzalezterreros, Blanca Ramirezbarajas, Yendi E Navarronoya, Luis M SanchezrodriguezAbstract:Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, i.e. inorganic fertilization, tillage, crop residue removal and maize (Zea mays L.) monoculture, and traditional organic farmed soil “milpa”, i.e. minimum tillage, rotation of maize, pumpkin (Cucurbita sp.) and beans (Phaseolus vulgaris L.) and organic fertilization were sampled. Both soils from the central highlands of Mexico were characterized and incubated aerobically at 5% field capacity (5%FC) and 100% field capacity (FC) for 45 days, while the C and N mineralization, enzyme activity and the bacterial community structure were monitored. After applying the different agricultural practices three years, the organic C content was 1.8-times larger in the milpa than in the conventional cultivated soil, the microbial biomass C 1.3-times, and C and N mineralization 2.0-times (mean for soil incubated at 5%FC and FC). The dehydrogenase, urease, protease and acid phosphatase activity was higher in the conventional cultivated soil than in the milpa soil incubated at 5%FC and similar when incubated at FC. The relative abundance of Gemmatimonadetes was larger in the conventional cultivated soil than in the milpa soil in soil both at 5%FC and FC, while that of Bacteroidetes showed an opposite trend. The relative abundance of other groups, such as Nitrospirae and Proteobacteria, was affected by cultivation technique, but controlled by soil water content. The relative abundance of other groups, e.g. FBP, Gemmatimonadetes and Proteobacteria, was affected by water content, but the effect depended on agricultural practice. For soil incubated at FC, the xenobiotics biodegradation and metabolism related functions were higher in the milpa soil than in the conventional cultivated soil, and carbohydrate metabolism showed an opposite trend. It was found that agricultural practices and soil water content had a strong effect on soil characteristics, C and N mineralization, enzyme activity, and the bacterial community structure and its functionality. The effect of soil water content on the bacterial community was defined often by the cultivation technique.
Yendi E. Navarro-noya - One of the best experts on this subject based on the ideXlab platform.
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Table_2_The Bacterial Community Structure and Microbial Activity in a Traditional Organic Milpa Farming System Under Different Soil Moisture Conditions.DOCX
2018Co-Authors: Iván P. Moreno-espíndola, Yendi E. Navarro-noya, María J. Ferrara-guerrero, Marco L. Luna-guido, Daniel A. Ramírez-villanueva, Arit S. De León-lorenzana, Selene Gómez-acata, Elizabeth González-terreros, Blanca Ramírez-barajas, Luis M. Sánchez-rodríguezAbstract:Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, i.e., inorganic fertilization, tillage, crop residue removal and maize (Zea mays L.) monoculture, and traditional organic farmed soil “milpa,” i.e., minimum tillage, rotation of maize, pumpkin (Cucurbita sp.) and beans (Phaseolus vulgaris L.) and organic fertilization were sampled. Both soils from the central highlands of Mexico were characterized and incubated aerobically at 5% field capacity (5ü) and 100% field capacity (FC) for 45 days, while the C and N mineralization, enzyme activity and the bacterial community structure were monitored. After applying the different agricultural practices 3 years, the organic C content was 1.8-times larger in the milpa than in the conventional cultivated soil, the microbial biomass C 1.3-times, and C and N mineralization 2.0-times (mean for soil incubated at 5ü and FC). The dehydrogenase, activity was significantly higher in the conventional cultivated soil than in the milpa soil when incubated at 5ü, but not when incubated at FC. The relative abundance of Gemmatimonadetes was larger in the conventional cultivated soil than in the milpa soil in soil both at 5ü and FC, while that of Bacteroidetes showed an opposite trend. The relative abundance of other groups, such as Nitrospirae and Proteobacteria, was affected by cultivation technique, but controlled by soil water content. The relative abundance of other groups, e.g., FBP, Gemmatimonadetes and Proteobacteria, was affected by water content, but the effect depended on agricultural practice. For soil incubated at FC, the xenobiotics biodegradation and metabolism related functions were higher in the milpa soil than in the conventional cultivated soil, and carbohydrate metabolism showed an opposite trend. It was found that agricultural practices and soil water content had a strong effect on soil characteristics, C and N mineralization, enzyme activity, and the bacterial community structure and its functionality. Decreases or increases in the relative abundance of bacterial groups when the soil water content decreased, i.e., from FC to 5ü, was defined often by the cultivation technique, and the larger organic matter content in the milpa soil did not prevent large changes in the bacterial community structure when the soil was dried.
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Image_2_The Bacterial Community Structure and Microbial Activity in a Traditional Organic Milpa Farming System Under Different Soil Moisture Conditions.JPEG
2018Co-Authors: Iván P. Moreno-espíndola, Yendi E. Navarro-noya, María J. Ferrara-guerrero, Marco L. Luna-guido, Daniel A. Ramírez-villanueva, Arit S. De León-lorenzana, Selene Gómez-acata, Elizabeth González-terreros, Blanca Ramírez-barajas, Luis M. Sánchez-rodríguezAbstract:Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, i.e., inorganic fertilization, tillage, crop residue removal and maize (Zea mays L.) monoculture, and traditional organic farmed soil “milpa,” i.e., minimum tillage, rotation of maize, pumpkin (Cucurbita sp.) and beans (Phaseolus vulgaris L.) and organic fertilization were sampled. Both soils from the central highlands of Mexico were characterized and incubated aerobically at 5% field capacity (5ü) and 100% field capacity (FC) for 45 days, while the C and N mineralization, enzyme activity and the bacterial community structure were monitored. After applying the different agricultural practices 3 years, the organic C content was 1.8-times larger in the milpa than in the conventional cultivated soil, the microbial biomass C 1.3-times, and C and N mineralization 2.0-times (mean for soil incubated at 5ü and FC). The dehydrogenase, activity was significantly higher in the conventional cultivated soil than in the milpa soil when incubated at 5ü, but not when incubated at FC. The relative abundance of Gemmatimonadetes was larger in the conventional cultivated soil than in the milpa soil in soil both at 5ü and FC, while that of Bacteroidetes showed an opposite trend. The relative abundance of other groups, such as Nitrospirae and Proteobacteria, was affected by cultivation technique, but controlled by soil water content. The relative abundance of other groups, e.g., FBP, Gemmatimonadetes and Proteobacteria, was affected by water content, but the effect depended on agricultural practice. For soil incubated at FC, the xenobiotics biodegradation and metabolism related functions were higher in the milpa soil than in the conventional cultivated soil, and carbohydrate metabolism showed an opposite trend. It was found that agricultural practices and soil water content had a strong effect on soil characteristics, C and N mineralization, enzyme activity, and the bacterial community structure and its functionality. Decreases or increases in the relative abundance of bacterial groups when the soil water content decreased, i.e., from FC to 5ü, was defined often by the cultivation technique, and the larger organic matter content in the milpa soil did not prevent large changes in the bacterial community structure when the soil was dried.
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Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils.
PloS one, 2016Co-Authors: Laura Delgado-balbuena, Yendi E. Navarro-noya, Marco Luna-guido, Juan Manuel Bello-lópez, Analine Rodríguez-valentín, Luc DendoovenAbstract:Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the effect of application of carrot residue, earthworms or the surfactant on the bacterial community structure was more accentuated in the arable soil than in the pasture soil. It was found that removal of anthracene was not linked to changes in the bacterial community structure.
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Modifications of bacterial populations in anthracene contaminated soil
Applied Soil Ecology, 2012Co-Authors: Edgar Vázquez Núñez, César Valenzuela-encinas, Rocío Alcántara-hernández, Yendi E. Navarro-noya, Marco Luna-guido, Rodolfo Marsch, Luc DendoovenAbstract:a b s t r a c t Spiking soil with anthracene, a polycyclic aromatic hydrocarbon, inhibited soil microbial activity, so it remained to be seen if the bacterial population composition was affected. An initial PCR-DGGE analysis indicated that the bacterial population in the unamended soil was not affected by depth (0–2 cm, 2–8 cm and 8–15 cm) or incubation time (0, 14 or 28 days) while it changed in the contaminated soil over the time and after 28 days in the soil profile. A phylogenetic analysis was done of the uncontaminated soil at day 0, and in the 0–2 cm layer of the anthracene-spiked soil after 0, 14 and 28 days and in the 2–8 cm layer after 28 days. Sequences belonged to six different phyla, i.e. Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae and Proteobacteria. However, 10% of the sequences remained as unclassified bacteria. Bacteria belonging to the Proteobacteria (63.2%) were always the most dominant followed by the Acidobacteria (22.8%) and the Gemmatimonadetes (3.6%). The percentage of Actinobacteria (4.1%), Chloroflexi (1.3%), and Nitrospirae (0.1%) was low and sequences belonging to these phyla were not always detected. Contaminating the soil had a momentaneous effect on the bacterial population as the percentage of Alphaproteobacteria, i.e. Sphingomonadales, and Gammaproteobacteria, i.e. the Xanthomonadales, reduced strongly while the percentage of Actinobacteria and Acidobacteria more than doubled. Already after 14 days, however, the percentage of Sphingomonadales, Actinobacteria and Acidobacteria was similar as in the unamended soil at day 0. After 28 days, the percentage of Burkholderiales and Xanthomonadales more than doubled in the 0–2 cm and 2–8 cm layer compared to the unamended soil at day 0. It was found that spiking soil with anthracene, incubation time and soil layer had an effect on the bacterial population, but the effect of the contaminant was transient and changes in the bacterial population with depth were only detectable in the contaminated soil after 28 days.
Xiaoliang Fan - One of the best experts on this subject based on the ideXlab platform.
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Bacteria with Different Assemblages in the Soil Profile Drive the Diverse Nutrient Cycles in the Sugarcane Straw Retention Ecosystem
Diversity, 2019Co-Authors: Caifang Zhang, Muhammad Tayyab, Ahmad Yusuf Abubakar, Ziqi Yang, Ziqin Pang, Waqar Islam, Zhaoli Lin, Jun Luo, Xiaoliang FanAbstract:Straw retention, an alternative to artificial fertilization, commonly mitigates soil degradation and positively affects soil fertility. In this study, we investigated the succession of soil bacteria during two sugarcane straw retention treatments (control (CK) and sugarcane straw retention (SR)) and at four depths (0–10, 10–20, 20–30, and 30–40 cm) in fallow soil in a sugarcane cropping system. Using an Illumina MiSeq (16S rRNA) and soil enzyme activity, we explored the SR influence on soil bacterial communities and enzyme activities and its inclusive impact on soil fertility, with an emphasis on topsoil (0–10 cm) and subsoil (10–40 cm). Our results show that SR effectively improved soil fertility indicators (C, N, and P), including enzyme activities (C and N cycling), throughout the soil profile: these soil parameters greatly improved in the topsoil compared to the control. Sugarcane straw retention and soil depth (0–10 cm vs. 10–40 cm) were associated with little variation in bacterial species richness and alpha diversity throughout the soil profile. Subsoil and topsoil bacterial communities differed in composition. Compared to the CK treatment, SR enriched the topsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, and Nitrospirae, while the subsoil was depleted in Nitrospirae and Acidobacteria. Similarly, SR enriched the subsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes, while the topsoil was depleted in Acidobacteria, Gemmatimonadetes, and Planctomycetes compared to the CK. At the genus level, SR enriched the topsoil with Gp1, Gp2, Gp5, Gp7, Gemmatimonas, Kofleria, Sphingomonas, and Gaiella, which decompose lignocellulose and contribute to nutrient cycling. In summary, SR not only improved soil physicochemical properties and enzyme activities but also enriched bacterial taxa involved in lignocellulosic decomposition and nutrient cycling (C and N) throughout the soil profile. However, these effects were stronger in topsoil than in subsoil, suggesting that SR enhanced fertility more in topsoil than in subsoil in fallow land.