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Tomazelli D, Klauberg-Filho O, Mendes LW, Goss-Souza D. The impact of land-use changes and management intensification on bacterial communities in the last decade: a review. Appl Environ Microbiol 2024; 90:e0030924. [PMID: 38874336 PMCID: PMC11267915 DOI: 10.1128/aem.00309-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024] Open
Abstract
In the last decade, advances in soil bacterial ecology have contributed to increasing agricultural production. Brazil is the world leading agriculture producer and leading soil biodiversity reservoir. Meanwhile, there is still a significant gap in the knowledge regarding the soil microscopic life and its interactions with agricultural practices, and the replacement of natural vegetation by agroecosystems is yet to be unfolded. Through high throughput DNA sequencing, scientists are now exploring the complexity of soil bacterial communities and their relationship with soil and environmental characteristics. This study aimed to investigate the progress of bacterial ecology studies in Brazil over the last 10 years, seeking to understand the effect of the conversion of natural vegetation in agricultural systems on the diversity and structure of the soil microbial communities. We conducted a systematic search for scientific publication databases. Our systematic search has matched 62 scientific articles from three different databases. Most of the studies were placed in southeastern and northern Brazil, with no records of studies about microbial ecology in 17 out of 27 Brazilian states. Out of the 26 studies that examined the effects of replacing natural vegetation with agroecosystems, most authors concluded that changes in soil pH and vegetation cover replacement were the primary drivers of shifts in microbial communities. Understanding the ecology of the bacteria inhabiting Brazilian soils in agroecosystems is paramount for developing more efficient soil management strategies and cleaner agricultural technologies.
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Affiliation(s)
- Daniela Tomazelli
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, Santa Catarina, Brazil
| | - Osmar Klauberg-Filho
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, Santa Catarina, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Dennis Goss-Souza
- College of Agronomy, Federal Institute of Paraná, Palmas, Paraná, Brazil
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Dietrich M, Panhölzl C, Angel R, Giguere AT, Randi D, Hausmann B, Herbold CW, Pötsch EM, Schaumberger A, Eichorst SA, Woebken D. Plant roots affect free-living diazotroph communities in temperate grassland soils despite decades of fertilization. Commun Biol 2024; 7:846. [PMID: 38987659 PMCID: PMC11237082 DOI: 10.1038/s42003-024-06522-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Fixation of atmospheric N2 by free-living diazotrophs accounts for an important proportion of nitrogen naturally introduced to temperate grasslands. The effect of plants or fertilization on the general microbial community has been extensively studied, yet an understanding of the potential combinatorial effects on the community structure and activity of free-living diazotrophs is lacking. In this study we provide a multilevel assessment of the single and interactive effects of different long-term fertilization treatments, plant species and vicinity to roots on the free-living diazotroph community in relation to the general microbial community in grassland soils. We sequenced the dinitrogenase reductase (nifH) and the 16S rRNA genes of bulk soil and root-associated compartments (rhizosphere soil, rhizoplane and root) of two grass species (Arrhenatherum elatius and Anthoxanthum odoratum) and two herb species (Galium album and Plantago lanceolata) growing in Austrian grassland soils treated with different fertilizers (N, P, NPK) since 1960. Overall, fertilization has the strongest effect on the diazotroph and general microbial community structure, however with vicinity to the root, the plant effect increases. Despite the long-term fertilization, plants strongly influence the diazotroph communities emphasizing the complexity of soil microbial communities' responses to changing nutrient conditions in temperate grasslands.
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Affiliation(s)
- Marlies Dietrich
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Christopher Panhölzl
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
| | - Andrew T Giguere
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dania Randi
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Te Kura Pūtaiao Koiora, School of Biological Sciences, Te Whare Wānanga o Waitaha, University of Canterbury, Christchurch, New Zealand
| | - Erich M Pötsch
- Institute of Plant Production and Cultural Landscape, Agricultural Research and Education Centre, Raumberg-Gumpenstein, Austria
| | - Andreas Schaumberger
- Institute of Plant Production and Cultural Landscape, Agricultural Research and Education Centre, Raumberg-Gumpenstein, Austria
| | - Stephanie A Eichorst
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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Thompson CC, Tschoeke D, Coutinho FH, Leomil L, Garcia GD, Otsuki K, Turcq BJ, Moreira LS, Turcq PFM, Cordeiro RC, Asp NE, Thompson FL. Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment. MICROBIAL ECOLOGY 2023; 86:2202-2209. [PMID: 37017718 DOI: 10.1007/s00248-023-02202-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.
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Affiliation(s)
- Cristiane C Thompson
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Diogo Tschoeke
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Biomedical Engineer Program, COPPE (UFRJ), Rio de Janeiro, Brazil
| | - Felipe H Coutinho
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Luciana Leomil
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gizele D Garcia
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Instituto de Ciências Médicas, Centro Multidisciplinar UFRJ Macae, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Macae, Brazil
| | - Koko Otsuki
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno J Turcq
- Institute de Recherche pour Le Dévelopment-Sorbonne, Université (UPMC, CNRS, IRD, MNHN) LOCEAN - Centre IRD France Nord, Bondy, France
| | - Luciane S Moreira
- Programa de Geoquímica, Universidade Federal Fluminense (UFF), Niterói, Rio de Janeiro, Brazil
| | - Patrícia F M Turcq
- Institute de Recherche pour Le Dévelopment-Sorbonne, Université (UPMC, CNRS, IRD, MNHN) LOCEAN - Centre IRD France Nord, Bondy, France
| | - Renato C Cordeiro
- Programa de Geoquímica, Universidade Federal Fluminense (UFF), Niterói, Rio de Janeiro, Brazil
| | - Nils E Asp
- Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará (UFPA), Bragança, Brazil
| | - Fabiano L Thompson
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Goss-Souza D, Tsai SM, Rodrigues JLM, Klauberg-Filho O, Sousa JP, Baretta D, Mendes LW. Biogeographic responses and niche occupancy of microbial communities following long-term land-use change. Antonie Van Leeuwenhoek 2022; 115:1129-1150. [DOI: 10.1007/s10482-022-01761-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/29/2022] [Indexed: 10/17/2022]
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Yan J, Han X, Lu X, Chen X, Zou W. Land use indirectly affects the cycling of multiple nutrients by altering the diazotrophic community in black soil. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3788-3795. [PMID: 34921680 DOI: 10.1002/jsfa.11727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/10/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Diazotrophic bacteria, as one of most important group of soil microorganisms, play critical roles in multiple ecosystem functions (i.e., multifunctionality). However, little information is available about the diazotrophic community in driving soil nutrient cycling and multifunctionality at different depths with distinct vegetation in the black soil region of northeastern China. To learn the interactions among land use, cycling of multiple nutrients and the diazotrophic community, we performed this study in grassland (GL), forested land and a cropland (CL) in soils at depths of 0-15 cm and 15-35 cm. RESULTS The highest nifH gene abundances were found in the CL treatment, while the highest diazotrophic species richness and diversity were detected in the GL in both soil layers. The nifH gene abundance was directly/positively correlated with soil bulk density and negatively correlated with land use and soil depth. The index of multiple nutrient cycling was directly/negatively affected by soil depth and indirectly/positively affected by land use. Land use directly/negatively affected soil pH and thus indirectly affected the diazotrophic community composition and the nutrient cycling index. The diversity and community composition of the diazotrophs together accounted for 95% of the differences in the multiple nutrient cycling index. CONCLUSION Soil diazotrophic communities undertake important roles in maintaining nutrient cycling and soil multifunctionality at depths of 0-15 cm and 15-35 cm layers with different land uses of the black soil region of China. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaozeng Han
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xinchun Lu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xu Chen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Wenxiu Zou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Mayhood P, Mirza BS. Soybean Root Nodule and Rhizosphere Microbiome: Distribution of Rhizobial and Nonrhizobial Endophytes. Appl Environ Microbiol 2021; 87:e02884-20. [PMID: 33674438 PMCID: PMC8117765 DOI: 10.1128/aem.02884-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/02/2021] [Indexed: 11/20/2022] Open
Abstract
Soybean root nodules are known to contain a high diversity of both rhizobial endophytes and nonrhizobial endophytes (NREs). Nevertheless, the variation of these bacteria among different root nodules within single plants has not been reported. So far, it is unclear whether the selection of NREs among different root nodules within single plants is a random process or is strictly controlled by the host plant to favor a few specific NREs based on their beneficial influence on plant growth. As well, it is also unknown if the relative frequency of NREs within different root nodules is consistent or if it varies based on the location or size of a root nodule. We assessed the microbiomes of 193 individual soybean root nodules from nine plants using high-throughput DNA sequencing. Bradyrhizobium japonicum strains occurred in high abundance in all root nodules despite the presence of other soybean-compatible rhizobia, such as Ensifer, Mesorhizobium, and other species of Bradyrhizobium in soil. Nitrobacter and Tardiphaga were the two nonrhizobial genera that were uniformly detected within almost all root nodules, though they were in low abundance. DNA sequences related to other NREs that have frequently been reported, such as Bacillus, Pseudomonas, Flavobacterium, and Variovorax species, were detected in a few nodules. Unlike for Bradyrhizobium, the low abundance and inconsistent occurrence of previously reported NREs among different root nodules within single plants suggest that these microbes are not preferentially selected as endophytes by host plants and most likely play a limited part in plant growth as endophytes.IMPORTANCE Soybean (Glycine max L.) is a valuable food crop that also contributes significantly to soil nitrogen by developing a symbiotic association with nitrogen-fixing rhizobia. Bacterial endophytes (both rhizobial and nonrhizobial) are considered critical for the growth and resilience of the legume host. In the past, several studies have suggested that the selection of bacterial endophytes within root nodules can be influenced by factors such as soil pH, nutrient availability, host plant genotype, and bacterial diversity in soil. However, the influence of size or location of root nodules on the selection of bacterial endophytes within soybean roots is unknown. It is also unclear whether the selection of nonrhizobial endophytes within different root nodules of a single plant is a random process or is strictly regulated by the host. This information can be useful in identifying potential bacterial species for developing bioinoculants that can enhance plant growth and soil nitrogen.
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Affiliation(s)
- Parris Mayhood
- Department of Biology, Missouri State University, Springfield, Missouri, USA
| | - Babur S Mirza
- Department of Biology, Missouri State University, Springfield, Missouri, USA
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