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Costa GXR, Silva LCF, de Oliveira LM, Santos LD. Microbiota of arabica coffee: insights from soil to fruit. World J Microbiol Biotechnol 2024; 40:308. [PMID: 39172263 DOI: 10.1007/s11274-024-04110-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 08/11/2024] [Indexed: 08/23/2024]
Abstract
Studies have shown that a diverse and metabolically active microbiota exists throughout different stages of coffee processing, from pre- to post-harvest. This microbiota originates from both the cultivation and processing environments. Additionally, microorganisms from the soil can be found on the fruit due to the transfer between them. This study reviews the microbiota present in Arabica coffee fruits and the soils where the plants are grown. It examines how microbial profiles are related to coffee variety, altitude, cultivation region, and processing method, and establishes a connection between the microbiota in soil and fruit. A diverse microbiota was observed in both coffee fruits and soils, with similar microorganisms identified across different growing regions, processing methods, and coffee varieties. However, exclusive detections of some microorganisms were also observed. These differences highlight the influence of terroir on coffee's microbial composition, confirming that environmental conditions, genetic factors, and processing methods shape coffee microbiota. Since microbial development during coffee fermentation can affect the beverage's quality, the data presented in this review offer valuable insights for researchers and producers. Understanding the influence of processing methods, coffee varieties, and cultivation regions on coffee microbiota enables the selection of specific fermentation conditions or starter cultures to enhance terroir characteristics or adjust microbial populations to favor or introduce microorganisms beneficial for coffee quality.
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Affiliation(s)
- Gisele Xavier Ribeiro Costa
- Faculty of Chemical Engineering, Federal University of Uberlândia (UFU), Patos de Minas - Minas Gerais, Uberlândia, Brazil
| | - Lívia Carneiro Fidélis Silva
- Institute of Biotechnology, Federal University of Uberlândia (UFU), Patos de Minas - Minas Gerais, Uberlândia, Brazil
| | - Liliane Maciel de Oliveira
- Department of Food Engineering, Federal University of São João del-Rei - UFSJ, Sete Lagoas - Minas Gerais, 47, MG 424 road, Sete Lagoas, Uberlândia, 35701-970, mailbox 56, MG, Brazil.
| | - Líbia Diniz Santos
- Faculty of Chemical Engineering, Federal University of Uberlândia (UFU), Patos de Minas - Minas Gerais, Uberlândia, Brazil
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Kruczyńska A, Kuźniar A, Banach A, Jurczyk S, Podlewski J, Słomczewski A, Marzec-Grządziel A, Sochaczewska A, Gałązka A, Wolińska A. Changes in the mycobiome structure in response to reduced nitrogen fertilization in two cropping systems of maize. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166343. [PMID: 37591379 DOI: 10.1016/j.scitotenv.2023.166343] [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: 05/29/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Nitrogen (N) is an essential element for plant productivity; hence, it is abundantly applied to the soil in the form of organic or chemical fertilizers, which consequently have a negative impact on the environment. Therefore, the main objective of our study was to investigate the structure and richness of the soil mycobiome in response to reduced nitrogen fertilization under two cropping systems: plowing (P) and no-till (NT). Moreover, the scope of the study perfectly falls into the EU "From Field to Table" strategy, which recommends a 20 % reduction of nitrogen fertilization of agricultural soils by 2030. In our study, the samples were collected twice during a single growing season: before maize sowing (without fertilization) and after harvesting the crop (four different fertilization rates). The mycobiome structure was identified based on the next generation sequencing (NGS) technique. Overall, our research has proved that the cropping system is important in terms of the formation of the fungal mycobiome structure and relative abundance. In addition, we confirmed that soil properties have a significant impact on fungal communities. We determined that a 20 % lower nitrogen fertilization rate (92.0 kg N ha-1) had a positive effect on the abundance of fungal communities. Moreover, the highest biodiversity at each of the taxonomic levels tested (phylum, class, genus) in the NT system and at the class and genus levels in the P system was also evidenced at the 20 % lower N fertilization rate. We also recommended potential indicators confirming the positive impact of reduced fertilization in two cropping systems: plowing - Epicoccum, Metarhizium, Mycosphaerella, and Paraconiothyrium and no-till - Peziza, Podospora, Metarhizium, Trechispora, and Umbelopsis.
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Affiliation(s)
- Anna Kruczyńska
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., Lublin, Poland.
| | - Agnieszka Kuźniar
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., Lublin, Poland.
| | - Artur Banach
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., Lublin, Poland.
| | - Sara Jurczyk
- Department of Artificial Intelligence, The John Paul II Catholic University of Lublin, Konstantynów 1 H Str., Lublin, Poland.
| | - Jacek Podlewski
- Potulicka Foundation Economic Center, Wojnowo 5, Sicienko, Poland.
| | | | - Anna Marzec-Grządziel
- Institute of Soil Science and Plant Cultivation, Department of Agriculture Microbiology, Czartoryskich 8 Str., 24-100 Puławy, Poland.
| | - Anna Sochaczewska
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., Lublin, Poland.
| | - Anna Gałązka
- Institute of Soil Science and Plant Cultivation, Department of Agriculture Microbiology, Czartoryskich 8 Str., 24-100 Puławy, Poland.
| | - Agnieszka Wolińska
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów 1 I Str., Lublin, Poland.
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de Souza TAF, da Silva LJR, Laurindo LK, Nascimento GDS, Campos MCC. Impact of ecological stages on the soil microbiota and soil abiotic factors in tropical and subtropical Brazilian regions. Arch Microbiol 2023; 205:335. [PMID: 37735302 DOI: 10.1007/s00203-023-03677-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/09/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023]
Abstract
Our aim was to test if ecological stages may influence the arbuscular mycorrhizal fungi (AMF), nematodes, and the soil chemical properties in agroforestry systems (AF), unassisted forest restoration (UFR), and natural ecosystem (Ne) located in the Brazilian Tropical and Subtropical regions. We collected soil samples to determine AMF, nematodes, soil pH, P, and soil organic carbon (SOC). AMF and nematode richness in the AF and Ne were similar in the tropical region. The redundancy analysis (RDA) indicated that the abundance of AMF and soil nematodes was mainly affected by soil pH, P, and SOC. Differences were associated with (1) ecological stages, as we found differences in AMF and nematode abundance as affected by habitat simplification, and (2) changes in soil pH, SOC, and P. Our work increases the understanding of the AMF and soil nematode community in the rhizosphere of AF and Ne in tropical and subtropical regions.
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Affiliation(s)
- Tancredo Augusto Feitosa de Souza
- Postgraduate Program in Soil Science, Department of Soils and Rural Engineering, Federal University of Paraiba, Areia, Paraiba, 58397-000, Brazil.
| | - Lucas Jónatan Rodrigues da Silva
- Postgraduate Program in Agrarian and Natural Ecosystems, Department of Agriculture, Biodiversity and Forests, Federal University of Santa Catarina, Curitibanos, Santa Catarina, 89520-000, Brazil
| | - Lídia Klestadt Laurindo
- Postgraduate Program in Agrarian and Natural Ecosystems, Department of Agriculture, Biodiversity and Forests, Federal University of Santa Catarina, Curitibanos, Santa Catarina, 89520-000, Brazil
| | - Gislaine Dos Santos Nascimento
- Postgraduate Program in Soil Science, Department of Soils and Rural Engineering, Federal University of Paraiba, Areia, Paraiba, 58397-000, Brazil
| | - Milton César Costa Campos
- Department of Soil and Rural Engineering, Centre of Agrarian Sciences, Federal University of Paraiba, Areia, Paraiba, 58397-000, Brazil
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Rawson C, Zahn G. Inclusion of database outgroups reduces false positives in fungal metabarcoding taxonomic assignments. Mycologia 2023:1-7. [PMID: 37196170 DOI: 10.1080/00275514.2023.2206931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
Metabarcoding studies of fungal communities rely on curated databases for assigning taxonomy. Any host or other nonfungal environmental sequences that are amplified during polymerase chain reaction (PCR) are inherently assigned taxonomy by these same databases, possibly leading to ambiguous nonfungal amplicons being assigned to fungal taxa. Here, we investigated the effects of including nonfungal outgroups in a fungal taxonomic database to aid in detecting and removing these nontarget amplicons. We processed 15 publicly available fungal metabarcode data sets and discovered that roughly 40% of the reads from these studies were not fungal, although they were assigned as Fungus sp. when using a database without nonfungal outgroups. We discuss implications for metabarcoding studies and recommend assigning taxonomy using a database with outgroups to better detect these nonfungal amplicons.
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Affiliation(s)
- Clayton Rawson
- Department of Biology, Utah Valley University, 800 W University Parkway, SB243, Orem, Utah 84058
| | - Geoffrey Zahn
- Department of Biology, Utah Valley University, 800 W University Parkway, SB243, Orem, Utah 84058
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Chen J, Shi Z, Liu S, Zhang M, Cao X, Chen M, Xu G, Xing H, Li F, Feng Q. Altitudinal Variation Influences Soil Fungal Community Composition and Diversity in Alpine-Gorge Region on the Eastern Qinghai-Tibetan Plateau. J Fungi (Basel) 2022; 8:807. [PMID: 36012795 PMCID: PMC9410234 DOI: 10.3390/jof8080807] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/04/2022] Open
Abstract
Soil fungi play an integral and essential role in maintaining soil ecosystem functions. The understanding of altitude variations and their drivers of soil fungal community composition and diversity remains relatively unclear. Mountains provide an open, natural platform for studying how the soil fungal community responds to climatic variability at a short altitude distance. Using the Illumina MiSeq high-throughput sequencing technique, we examined soil fungal community composition and diversity among seven vegetation types (dry valley shrub, valley-mountain ecotone broadleaved mixed forest, subalpine broadleaved mixed forest, subalpine coniferous-broadleaved mixed forest, subalpine coniferous forest, alpine shrub meadow, alpine meadow) along a 2582 m altitude gradient in the alpine-gorge region on the eastern Qinghai-Tibetan Plateau. Ascomycota (47.72%), Basidiomycota (36.58%), and Mortierellomycota (12.14%) were the top three soil fungal dominant phyla in all samples. Soil fungal community composition differed significantly among the seven vegetation types along altitude gradients. The α-diversity of soil total fungi and symbiotic fungi had a distinct hollow pattern, while saprophytic fungi and pathogenic fungi showed no obvious pattern along altitude gradients. The β-diversity of soil total fungi, symbiotic fungi, saprophytic fungi, and pathogenic fungi was derived mainly from species turnover processes and exhibited a significant altitude distance-decay pattern. Soil properties explained 31.27-34.91% of variation in soil fungal (total and trophic modes) community composition along altitude gradients, and the effects of soil nutrients on fungal community composition varied by trophic modes. Soil pH was the main factor affecting α-diversity of soil fungi along altitude gradients. The β-diversity and turnover components of soil total fungi and saprophytic fungi were affected by soil properties and geographic distance, while those of symbiotic fungi and pathogenic fungi were affected only by soil properties. This study deepens our knowledge regarding altitude variations and their drivers of soil fungal community composition and diversity, and confirms that the effects of soil properties on soil fungal community composition and diversity vary by trophic modes along altitude gradients in the alpine-gorge region.
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Affiliation(s)
- Jian Chen
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Zuomin Shi
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy
| | - Shun Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Miaomiao Zhang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Xiangwen Cao
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Miao Chen
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Gexi Xu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Hongshuang Xing
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Feifan Li
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Qiuhong Feng
- Ecological Restoration and Conservation on Forest and Wetland Key Laboratory of Sichuan Province, Sichuan Academy of Forestry, Chengdu 610081, China;
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