Pub Date : 2024-01-17DOI: 10.1186/s13213-024-01749-8
Giulia Zardinoni, Saptarathi Deb, Samathmika Ravi, Lucia Giagnoni, Piergiorgio Fumelli, Alessandra Tondello, Mauro Dacasto, Andrea Squartini, Carlo Spanu, Angela Trocino, Piergiorgio Stevanato
Lagoons are important natural systems, with attractive favorable conditions for aquaculture production, such as shellfish cultivation. Despite their socio-economic relevance for human activity, information on the microbial diversity, community composition, and putative functions of gill-associated microbiota and seawater is still limited, particularly as regards the extent of specific taxa enrichment within the gills and the relative effects of the temporal and spatial variables. In this study, we used a 16S rDNA multi-amplicon sequencing approach using an Ion GeneStudio S5 System and a function prediction method (Functional Annotation of Prokaryotic Taxa (FAPROTAX), to inspect the springtime dynamics of microbial communities and their inferred metabolic features in an Adriatic lagoon (Po Delta, Italy). Mussels and surrounding seawater were sampled in two rearing areas three times between April and June 2021. Sequencing results showed significant (p ≤ 0.05) differences in bacterial community composition and diversity between gills and seawater. Gills were dominated by the Methylobacterium-Methylorubrum and Burkholderia-Caballeronia-Paraburkholderia genera, while in seawater samples Izamaplasma, Planktomarina, and Candidatus Aquiluna were detected as being dominant. The microbiota composition did not differ significantly between the two rearing areas. The sampling time, although limited to a 3-month timeframe, instead revealed a structural variation of the bacterial profile both in gills and seawater for alpha and beta diversities respectively. The functional prediction analysis highlighted an overexpression of human gut-associated bacteria in relation to the season-related increase in seawater temperature. These findings enhance our understanding of the differences between gill-associated and seawater microbiota composition and provide novel insights into the functions carried out by bacteria inhabiting these niches, as well as on the key host-symbiont relationships of bivalves in lagoon environments.
{"title":"Difference in composition and functional analysis of bacterial communities between Mytilus galloprovincialis gills and surrounding water in a brackish inshore bay, analyzed by 16S rDNA multi-amplicon sequencing","authors":"Giulia Zardinoni, Saptarathi Deb, Samathmika Ravi, Lucia Giagnoni, Piergiorgio Fumelli, Alessandra Tondello, Mauro Dacasto, Andrea Squartini, Carlo Spanu, Angela Trocino, Piergiorgio Stevanato","doi":"10.1186/s13213-024-01749-8","DOIUrl":"https://doi.org/10.1186/s13213-024-01749-8","url":null,"abstract":"Lagoons are important natural systems, with attractive favorable conditions for aquaculture production, such as shellfish cultivation. Despite their socio-economic relevance for human activity, information on the microbial diversity, community composition, and putative functions of gill-associated microbiota and seawater is still limited, particularly as regards the extent of specific taxa enrichment within the gills and the relative effects of the temporal and spatial variables. In this study, we used a 16S rDNA multi-amplicon sequencing approach using an Ion GeneStudio S5 System and a function prediction method (Functional Annotation of Prokaryotic Taxa (FAPROTAX), to inspect the springtime dynamics of microbial communities and their inferred metabolic features in an Adriatic lagoon (Po Delta, Italy). Mussels and surrounding seawater were sampled in two rearing areas three times between April and June 2021. Sequencing results showed significant (p ≤ 0.05) differences in bacterial community composition and diversity between gills and seawater. Gills were dominated by the Methylobacterium-Methylorubrum and Burkholderia-Caballeronia-Paraburkholderia genera, while in seawater samples Izamaplasma, Planktomarina, and Candidatus Aquiluna were detected as being dominant. The microbiota composition did not differ significantly between the two rearing areas. The sampling time, although limited to a 3-month timeframe, instead revealed a structural variation of the bacterial profile both in gills and seawater for alpha and beta diversities respectively. The functional prediction analysis highlighted an overexpression of human gut-associated bacteria in relation to the season-related increase in seawater temperature. These findings enhance our understanding of the differences between gill-associated and seawater microbiota composition and provide novel insights into the functions carried out by bacteria inhabiting these niches, as well as on the key host-symbiont relationships of bivalves in lagoon environments.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139483259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-13DOI: 10.1186/s13213-023-01747-2
Haisheng He, Sijia Bao, Yannan Wu, Deli Tong
{"title":"Remediation of copper-contaminated soils and growth enhancement of Pakchoi (B. chinensis L.) via biofertilizers composed of new Bacillus amyloliquefaciens SYNU1","authors":"Haisheng He, Sijia Bao, Yannan Wu, Deli Tong","doi":"10.1186/s13213-023-01747-2","DOIUrl":"https://doi.org/10.1186/s13213-023-01747-2","url":null,"abstract":"","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139437231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-03DOI: 10.1186/s13213-023-01744-5
Mansoor Khaledi, Behnam Poureslamfar, Hashem O. Alsaab, Shahrad Tafaghodi, Ahmed Hjazi, Rajesh Singh, Ahmed Hussien Alawadi, Ali Alsaalamy, Qutaiba A. Qasim, Fatemeh Sameni
The gut microbiota plays a crucial role in regulating the host’s immune responses during aging, which was characterized by a different abundance of bacteria in several age groups. Gut microbiota dysbiosis is associated with aging, antibiotic exposure, underlying diseases, infections, hormonal variations, circadian rhythm, and malnutrition, either singularly or in combination. The appropriate use of prebiotics and probiotics may be able to prevent or reduce this disruption. The current review focuses on the gut microbiota composition across the life cycle, factors affecting gut microbiota changes with aging, and interventions to modulate gut microbiota.
{"title":"The role of gut microbiota in human metabolism and inflammatory diseases: a focus on elderly individuals","authors":"Mansoor Khaledi, Behnam Poureslamfar, Hashem O. Alsaab, Shahrad Tafaghodi, Ahmed Hjazi, Rajesh Singh, Ahmed Hussien Alawadi, Ali Alsaalamy, Qutaiba A. Qasim, Fatemeh Sameni","doi":"10.1186/s13213-023-01744-5","DOIUrl":"https://doi.org/10.1186/s13213-023-01744-5","url":null,"abstract":"The gut microbiota plays a crucial role in regulating the host’s immune responses during aging, which was characterized by a different abundance of bacteria in several age groups. Gut microbiota dysbiosis is associated with aging, antibiotic exposure, underlying diseases, infections, hormonal variations, circadian rhythm, and malnutrition, either singularly or in combination. The appropriate use of prebiotics and probiotics may be able to prevent or reduce this disruption. The current review focuses on the gut microbiota composition across the life cycle, factors affecting gut microbiota changes with aging, and interventions to modulate gut microbiota.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139095209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-15DOI: 10.1186/s13213-023-01742-7
Jinmei Guo, Jianfeng Li, Shuqing Zhang, Ping Chen
To determine the differences in the microbial communities in the Camellia sinensis L. hairy root, lateral root, and main root rhizospheres in Anping Village, Kaiyang County, Guizhou Province, the community structure, diversity, and main dominant species of bacteria and fungi in different parts of the soil were analyzed by ITS and 16S sequencing. In the rhizosphere soil of the main root, lateral root, and hairy root of Camellia sinensis L., there were significant differences in the diversity and richness of the bacterial and fungal communities. The bacterial diversity was the highest and the fungal richness was the lowest in the rhizosphere soil of the main root. In the bacterial community, Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the common dominant bacteria. Rhodospirillaceae, Bradyrhizobiaceae, Hyphomicrobiaceae, Solibacteraceae, and Koribacteraceae were the common dominant bacteria in the rhizosphere soil of different parts of the root system, but the relative abundance of bacteria in different parts of the rhizosphere soil varied greatly. The dominant groups of fungal communities in different parts of the rhizosphere soil were Basidiomycota, Ascomycota, Mortierellomycota, and Sebacinaceae. The structure of the fungal community is similar in different parts. Compared with the different parts of the hairy root, lateral root, and main root of rhizosphere soil of Camellia sinensis L. in Anping village, it was found that the abundance of fungal community decreased with the increase of bacterial community abundance, and there were significant differences in bacterial community diversity and structure. However, the fungal community maintained stability among different parts.
{"title":"Study on the soil microbial community structure of the Rhizosphere of Camellia sinensis L. in Anping Village, Kaiyang County, Guizhou Province","authors":"Jinmei Guo, Jianfeng Li, Shuqing Zhang, Ping Chen","doi":"10.1186/s13213-023-01742-7","DOIUrl":"https://doi.org/10.1186/s13213-023-01742-7","url":null,"abstract":"To determine the differences in the microbial communities in the Camellia sinensis L. hairy root, lateral root, and main root rhizospheres in Anping Village, Kaiyang County, Guizhou Province, the community structure, diversity, and main dominant species of bacteria and fungi in different parts of the soil were analyzed by ITS and 16S sequencing. In the rhizosphere soil of the main root, lateral root, and hairy root of Camellia sinensis L., there were significant differences in the diversity and richness of the bacterial and fungal communities. The bacterial diversity was the highest and the fungal richness was the lowest in the rhizosphere soil of the main root. In the bacterial community, Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the common dominant bacteria. Rhodospirillaceae, Bradyrhizobiaceae, Hyphomicrobiaceae, Solibacteraceae, and Koribacteraceae were the common dominant bacteria in the rhizosphere soil of different parts of the root system, but the relative abundance of bacteria in different parts of the rhizosphere soil varied greatly. The dominant groups of fungal communities in different parts of the rhizosphere soil were Basidiomycota, Ascomycota, Mortierellomycota, and Sebacinaceae. The structure of the fungal community is similar in different parts. Compared with the different parts of the hairy root, lateral root, and main root of rhizosphere soil of Camellia sinensis L. in Anping village, it was found that the abundance of fungal community decreased with the increase of bacterial community abundance, and there were significant differences in bacterial community diversity and structure. However, the fungal community maintained stability among different parts.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138681181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-25DOI: 10.1186/s13213-023-01741-8
Gamachis Korsa, Abera Beyene, Abate Ayele
High population growth and the expansion of industry from time to time produce a large amount of waste/pollution, which harms global environmental health. To overcome the above problems, soil feeding (mound/nest) builders of termite gut bacteria execute thriving since they can be obtained easily, available, and at low costs. The purpose of this review is to provide evidence of bacteria in the soil feeding termite gut and its potential role in various applications including reduction of methane gas emission, bio bocks/production of bricks, biomedicine, biocontrol (promising tool for sustainable agriculture), and bio-fertilizer (improve the fertility of the soil) and plant growth promote effectiveness all year. This review was progressive in that it assessed and produced peer-reviewed papers related to bacteria in the soil feeding termite gut and its potential role in different applications for an environmentally sound. Based on the findings of reputable educational journals, articles were divided into four categories: methods used to distributions of soil-feeding termites, termite caste system, bacterial diversity, and strain improvement of bacteria in the termite guts for enhanced multipurpose and techniques. The bacterial diversity from termite guts of soil feeding termite caste systems/differentiations is vital for snowballing day to day due to their low cost and no side effect on the public health and environment becoming known improvement of the microbial bacteria rather than other microbes. So termites function as “soil engineers” in tropical agroforestry ecosystems that are of great benefit for economic importance to greener approach. The present findings indicate that recovery was chosen as an appreciable bring out the bacteria in the soil feeding termite gut and its potential application of termite mounds/nests biotechnological applications. Because of the large amount of nutrients that have built up in termite embankment soil feeding, this type of termite is now known as a “gold-leaf excavation” for bacterial concentrations. This provides the assertion that termite insects are important from an ecological standpoint since they aid in nutrient flows in the ecosystem as a useful tool for various species.
{"title":"Bacterial diversity from soil-feeding termite gut and their potential application","authors":"Gamachis Korsa, Abera Beyene, Abate Ayele","doi":"10.1186/s13213-023-01741-8","DOIUrl":"https://doi.org/10.1186/s13213-023-01741-8","url":null,"abstract":"High population growth and the expansion of industry from time to time produce a large amount of waste/pollution, which harms global environmental health. To overcome the above problems, soil feeding (mound/nest) builders of termite gut bacteria execute thriving since they can be obtained easily, available, and at low costs. The purpose of this review is to provide evidence of bacteria in the soil feeding termite gut and its potential role in various applications including reduction of methane gas emission, bio bocks/production of bricks, biomedicine, biocontrol (promising tool for sustainable agriculture), and bio-fertilizer (improve the fertility of the soil) and plant growth promote effectiveness all year. This review was progressive in that it assessed and produced peer-reviewed papers related to bacteria in the soil feeding termite gut and its potential role in different applications for an environmentally sound. Based on the findings of reputable educational journals, articles were divided into four categories: methods used to distributions of soil-feeding termites, termite caste system, bacterial diversity, and strain improvement of bacteria in the termite guts for enhanced multipurpose and techniques. The bacterial diversity from termite guts of soil feeding termite caste systems/differentiations is vital for snowballing day to day due to their low cost and no side effect on the public health and environment becoming known improvement of the microbial bacteria rather than other microbes. So termites function as “soil engineers” in tropical agroforestry ecosystems that are of great benefit for economic importance to greener approach. The present findings indicate that recovery was chosen as an appreciable bring out the bacteria in the soil feeding termite gut and its potential application of termite mounds/nests biotechnological applications. Because of the large amount of nutrients that have built up in termite embankment soil feeding, this type of termite is now known as a “gold-leaf excavation” for bacterial concentrations. This provides the assertion that termite insects are important from an ecological standpoint since they aid in nutrient flows in the ecosystem as a useful tool for various species.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138496553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-26DOI: 10.1186/s13213-023-01740-9
Desalegn Amenu, Ketema Bacha
Abstract Background Probiotics are live microorganisms that effectively combat foodborne pathogens, promoting intestinal health when consumed in sufficient amounts. This study evaluated the probiotic potential and safety of lactic acid bacteria isolated from selected Ethiopian traditional fermented foods and beverages (Kotcho, Bulla, Ergo, Cabbage-Shamita, Borde, and Bukuri). To assess the isolates’ probiotic activity, tolerance, and survival rate under various stressful conditions, including low pH, intestinal inhibitory substances, salt concentration, bile salt, and simulated gastric/intestinal juice. The isolates were also tested for antagonistic activities against common bacterial and fungal pathogens ( Staphylococcus aureus , Salmonella Typhimurium, Escherichia coli , Pseudomonas aeruginosa , Klebsiella pneumoniae , and Candida albicans ) and safety (auto-aggregation, co-aggregation, cell source hydrophobicity, hemolytic activity, DNase, and antibiotic susceptibility). The best probiotic lactic acid bacteria (LAB) were characterized to species level following standard MALDI TOF/mass spectrometry analysis. Results A total of 125 potentially probiotic LAB were isolated of which 17 (13.60%) isolates survived low pH (2, 2.5, and 3), bile salt (0.3%), intestinal inhibitory chemicals (phenol, bile, low acidity, pepsin, and pancreas), and simulated gastro-intestinal settings with near 60–94% survival rate. In addition, 11 best LAB isolates were further screened based on additional screening including their antimicrobial efficacy, preservative efficiency, bacteriocin production besides resistance to low acid and bile salts, and survival potential under simulated gastrointestinal conditions. All 11 LAB isolates were resistant to ampicillin, vancomycin, gentamicin, kanamycin, clindamycin, and chloramphenicol, while they were susceptible to streptomycin and tetracycline. The MALDI TOF mass spectrometry analysis result of efficient probiotic LAB grouped them under the genus Pediococcu s, Enterococcus , and Lactococcus including Pediococcus pentosaceus , Enterococcus faecium , Lactococcus lactis , and Pediococcus acidilactici . Conclusion Ethiopian traditional fermented foods and beverages are good sources of promising probiotic lactic acid bacteria. These isolates could serve as potential starter cultures and bio-preservative for the enhancement of the shelf life of foods. This study established the groundwork for the selection of excellent probiotics for the development and application of LAB for antibacterial action, starter culture production, and preservation activities.
{"title":"Probiotic potential and safety analysis of lactic acid bacteria isolated from Ethiopian traditional fermented foods and beverages","authors":"Desalegn Amenu, Ketema Bacha","doi":"10.1186/s13213-023-01740-9","DOIUrl":"https://doi.org/10.1186/s13213-023-01740-9","url":null,"abstract":"Abstract Background Probiotics are live microorganisms that effectively combat foodborne pathogens, promoting intestinal health when consumed in sufficient amounts. This study evaluated the probiotic potential and safety of lactic acid bacteria isolated from selected Ethiopian traditional fermented foods and beverages (Kotcho, Bulla, Ergo, Cabbage-Shamita, Borde, and Bukuri). To assess the isolates’ probiotic activity, tolerance, and survival rate under various stressful conditions, including low pH, intestinal inhibitory substances, salt concentration, bile salt, and simulated gastric/intestinal juice. The isolates were also tested for antagonistic activities against common bacterial and fungal pathogens ( Staphylococcus aureus , Salmonella Typhimurium, Escherichia coli , Pseudomonas aeruginosa , Klebsiella pneumoniae , and Candida albicans ) and safety (auto-aggregation, co-aggregation, cell source hydrophobicity, hemolytic activity, DNase, and antibiotic susceptibility). The best probiotic lactic acid bacteria (LAB) were characterized to species level following standard MALDI TOF/mass spectrometry analysis. Results A total of 125 potentially probiotic LAB were isolated of which 17 (13.60%) isolates survived low pH (2, 2.5, and 3), bile salt (0.3%), intestinal inhibitory chemicals (phenol, bile, low acidity, pepsin, and pancreas), and simulated gastro-intestinal settings with near 60–94% survival rate. In addition, 11 best LAB isolates were further screened based on additional screening including their antimicrobial efficacy, preservative efficiency, bacteriocin production besides resistance to low acid and bile salts, and survival potential under simulated gastrointestinal conditions. All 11 LAB isolates were resistant to ampicillin, vancomycin, gentamicin, kanamycin, clindamycin, and chloramphenicol, while they were susceptible to streptomycin and tetracycline. The MALDI TOF mass spectrometry analysis result of efficient probiotic LAB grouped them under the genus Pediococcu s, Enterococcus , and Lactococcus including Pediococcus pentosaceus , Enterococcus faecium , Lactococcus lactis , and Pediococcus acidilactici . Conclusion Ethiopian traditional fermented foods and beverages are good sources of promising probiotic lactic acid bacteria. These isolates could serve as potential starter cultures and bio-preservative for the enhancement of the shelf life of foods. This study established the groundwork for the selection of excellent probiotics for the development and application of LAB for antibacterial action, starter culture production, and preservation activities.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134909954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-14DOI: 10.1186/s13213-023-01738-3
Arifa Akhter Airin, Md Iyasir Arafat, Rifat Ara Begum, Md Rakibul Islam, Zeba Islam Seraj
Abstract Background Plant growth-promoting endophytic fungi (PGPEF) that are associated with halophytes have the potential to boost crop salinity tolerance and productivity. This in turn has the potential of enabling and improving cultivation practices in coastal lands affected by salt stress. Methods Endophytic fungi from the wild halophytic rice Oryza coarctata were isolated, characterized, identified, and studied for their effects on all developing stages of rice plant growth and their yields both with and without salt stress. Key results In this study, three different fungal endophytes were isolated from the halophytic wild rice Oryza coarctata . Two isolates were identified as Talaromyces adpressus (OPCRE2) and Talaromyces argentinensis (OPCRh1) by ITS region sequencing. The remaining isolate NPCRE2 was confirmed as a novel strain named Aspergillus welwitschiae Oc streb1 ( AwOc streb1) by whole genome sequencing. These endophytes showed various plant growth-promoting (PGP) abilities in vitro (e.g., IAA, ACC-deaminase and siderophore production, phosphate, and zinc solubilization as well as nitrogen fixation), where AwOc streb1 was significantly more efficient compared to the other two isolates at high salinity (900 mm). Independent application of these fungi in commercial rice ( Oryza sativa ) showed significant elevation in plant growth, especially in the case of the AwOc streb1 inoculants, which had enhanced metabolite and chlorophyll content at the seedling stage in both no-salt control and 100-m m salt-stressed plants. At the same time, AwOc streb1-treated plants had a significantly lower level of H 2 O 2 , electrolyte leakage, and Na + /K + ratio under saline conditions. Higher expression (1.6 folds) of the SOS1 (salt overly sensitive 1) gene was also observed in these plants under salinity stress. This strain also improved percent fertility, tillering, panicle number, and filled grain number in both no-salt control and 45-m m salt-stressed inoculated plants at the reproductive stage. Consequently, the differences in their yield was 125.16% and 203.96% ( p < 0.05) in colonized plants in normal and saline conditions, respectively, compared to uninoculated controls. Conclusions We propose that AwOc streb1 is a potential candidate for an eco-friendly biofertilizer formula to improve the cultivation and yield of rice or any other crop in the highly saline coastal regions of Bangladesh.
{"title":"Plant growth-promoting endophytic fungi of the wild halophytic rice Oryza coarctata","authors":"Arifa Akhter Airin, Md Iyasir Arafat, Rifat Ara Begum, Md Rakibul Islam, Zeba Islam Seraj","doi":"10.1186/s13213-023-01738-3","DOIUrl":"https://doi.org/10.1186/s13213-023-01738-3","url":null,"abstract":"Abstract Background Plant growth-promoting endophytic fungi (PGPEF) that are associated with halophytes have the potential to boost crop salinity tolerance and productivity. This in turn has the potential of enabling and improving cultivation practices in coastal lands affected by salt stress. Methods Endophytic fungi from the wild halophytic rice Oryza coarctata were isolated, characterized, identified, and studied for their effects on all developing stages of rice plant growth and their yields both with and without salt stress. Key results In this study, three different fungal endophytes were isolated from the halophytic wild rice Oryza coarctata . Two isolates were identified as Talaromyces adpressus (OPCRE2) and Talaromyces argentinensis (OPCRh1) by ITS region sequencing. The remaining isolate NPCRE2 was confirmed as a novel strain named Aspergillus welwitschiae Oc streb1 ( AwOc streb1) by whole genome sequencing. These endophytes showed various plant growth-promoting (PGP) abilities in vitro (e.g., IAA, ACC-deaminase and siderophore production, phosphate, and zinc solubilization as well as nitrogen fixation), where AwOc streb1 was significantly more efficient compared to the other two isolates at high salinity (900 mm). Independent application of these fungi in commercial rice ( Oryza sativa ) showed significant elevation in plant growth, especially in the case of the AwOc streb1 inoculants, which had enhanced metabolite and chlorophyll content at the seedling stage in both no-salt control and 100-m m salt-stressed plants. At the same time, AwOc streb1-treated plants had a significantly lower level of H 2 O 2 , electrolyte leakage, and Na + /K + ratio under saline conditions. Higher expression (1.6 folds) of the SOS1 (salt overly sensitive 1) gene was also observed in these plants under salinity stress. This strain also improved percent fertility, tillering, panicle number, and filled grain number in both no-salt control and 45-m m salt-stressed inoculated plants at the reproductive stage. Consequently, the differences in their yield was 125.16% and 203.96% ( p < 0.05) in colonized plants in normal and saline conditions, respectively, compared to uninoculated controls. Conclusions We propose that AwOc streb1 is a potential candidate for an eco-friendly biofertilizer formula to improve the cultivation and yield of rice or any other crop in the highly saline coastal regions of Bangladesh.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135766633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-13DOI: 10.1186/s13213-023-01739-2
Mohamed El-Khateeb, Gamal K. Hassan, Mohamed Azab El-Liethy, Kamel M. El-Khatib, Hussein I. Abdel-Shafy, Anyi Hu, Mahmoud Gad
Abstract Background The upflow anaerobic sludge blanket (UASB) reactors rely on bacterial communities to break down pollutants in wastewater (municipal or industrial). Methods and results In this study, a novel combination of UASB followed by aerobic treatment has been proposed for the treatment of municipal wastewater focusing on bacterial communities using high-throughput sequencing and parasite removal in this novel combination of reactors. Moreover, economic estimation of the compact unit composed of two overlapping UASB reactors, followed by a downflow hanging non-woven fabric (DHNW) reactor, the anaerobic baffled reactor (ABR), and chlorine unit was investigated in this study based on community populations of 1000 and 10,000 inhabitants, with a municipal plant capacity of 54,000 and 540,000 m 3 /year. Cost estimation was conducted based on two scenarios, one considering the contingency cost and auxiliary facility, and the other excluding them. Non-metric multidimensional scaling (nMDS) revealed that the treatment stages structured the microbial communities. Proteobacteria was the most prevalent phylum in all treatment stages, followed by Bacteroidota in most stages. Firmicutes and Actinobacteria were also present in significant amounts. The treatment system achieved from 40 to 66.67% removal of parasites (parasitic nematode, Cryptosporidium , and microsporidia). Redundancy analysis (RDA) indicated a strong positive correlation between chemical and biological oxygen demand (COD/BOD) with Campylobacterales and could be used as a bioindicator of treatment performance. Conclusion These findings can inform the development of more efficient and sustainable wastewater treatment systems that take into account microbial ecology and economic considerations.
{"title":"Sustainable municipal wastewater treatment using an innovative integrated compact unit: microbial communities, parasite removal, and techno-economic analysis","authors":"Mohamed El-Khateeb, Gamal K. Hassan, Mohamed Azab El-Liethy, Kamel M. El-Khatib, Hussein I. Abdel-Shafy, Anyi Hu, Mahmoud Gad","doi":"10.1186/s13213-023-01739-2","DOIUrl":"https://doi.org/10.1186/s13213-023-01739-2","url":null,"abstract":"Abstract Background The upflow anaerobic sludge blanket (UASB) reactors rely on bacterial communities to break down pollutants in wastewater (municipal or industrial). Methods and results In this study, a novel combination of UASB followed by aerobic treatment has been proposed for the treatment of municipal wastewater focusing on bacterial communities using high-throughput sequencing and parasite removal in this novel combination of reactors. Moreover, economic estimation of the compact unit composed of two overlapping UASB reactors, followed by a downflow hanging non-woven fabric (DHNW) reactor, the anaerobic baffled reactor (ABR), and chlorine unit was investigated in this study based on community populations of 1000 and 10,000 inhabitants, with a municipal plant capacity of 54,000 and 540,000 m 3 /year. Cost estimation was conducted based on two scenarios, one considering the contingency cost and auxiliary facility, and the other excluding them. Non-metric multidimensional scaling (nMDS) revealed that the treatment stages structured the microbial communities. Proteobacteria was the most prevalent phylum in all treatment stages, followed by Bacteroidota in most stages. Firmicutes and Actinobacteria were also present in significant amounts. The treatment system achieved from 40 to 66.67% removal of parasites (parasitic nematode, Cryptosporidium , and microsporidia). Redundancy analysis (RDA) indicated a strong positive correlation between chemical and biological oxygen demand (COD/BOD) with Campylobacterales and could be used as a bioindicator of treatment performance. Conclusion These findings can inform the development of more efficient and sustainable wastewater treatment systems that take into account microbial ecology and economic considerations.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135857084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-28DOI: 10.1186/s13213-023-01736-5
Muhammad Ahmad, Muhammad Imtiaz, Muhammad Shoib Nawaz, Fathia Mubeen, Yasra Sarwar, Mahnoor Hayat, Muhammad Asif, Rubab Zahra Naqvi, Muhammad Ahmad, Asma Imran
Abstract Background Global warming and irregular changes in temperature are a serious threat to plant growth with a significant negative impact on yield. Global maize productivity has decreased significantly due to sudden temperature fluctuations and heat waves especially in the regions severely hit by climate change. Results The current study demonstrates the potential of beneficial bacteria for inducing heat tolerance in maize during early growth. Three Bacillus spp . AH-08, AH-67, SH-16, and one Pseudomonas spp . SH-29 showed the ability to grow and exhibited multiple plant-beneficial traits up to 45 ± 2 °C. At temperatures of 45 and 50 °C, Bacillus sp. SH-16 exhibited upregulation of two small heat shock proteins (HSP) of 15 and 30 kDa, while SH-16 and AH-67 showed upregulation of two large HSP of 65 and 100 kDa. Plant-inoculation with the consortium B3P (3 Bacillus + 1 Pseudomonas spp.) was carried out on six hybrid maize varieties pre-grown at 25 ± 2 ºC. Heat shock was applied to 10-day-old seedlings as: 3 h at 38ºC, 48 h recovery period, and then 48 h at 42ºC. The B3P treatment showed significant improvement in the overall plant growth (plant height, root & shoot fresh & dry weight, root and leaf area) with a higher level of CAT, POD, total chlorophyll, and carotenoids, while low concentration of MDA. A non-significant difference was observed in case of total cell protein and amino acids after B3P-treatment under stress. The expression of HSP1 and HSP18 in Malka and YH-5427 while HSP70 and HSP101 were higher in FH-1046 and Gohar as compared to non-inoculated treatment. Conclusions These findings indicate that heat-tolerant plant-growth promoting rhizobacteria (Ht-PGPR) exert versatile, multiphasic and differential response to improve plant growth and heat-tolerance in different maize varieties during seedling/ early vegetative growth. Subsequent research will be focused on the field evaluation of these PGPR to see the field and yield response of this consortium under natural temperature fluctuations in field.
{"title":"Thermotolerant PGPR consortium B3P modulates physio-biochemical and molecular machinery for enhanced heat tolerance in maize during early vegetative growth","authors":"Muhammad Ahmad, Muhammad Imtiaz, Muhammad Shoib Nawaz, Fathia Mubeen, Yasra Sarwar, Mahnoor Hayat, Muhammad Asif, Rubab Zahra Naqvi, Muhammad Ahmad, Asma Imran","doi":"10.1186/s13213-023-01736-5","DOIUrl":"https://doi.org/10.1186/s13213-023-01736-5","url":null,"abstract":"Abstract Background Global warming and irregular changes in temperature are a serious threat to plant growth with a significant negative impact on yield. Global maize productivity has decreased significantly due to sudden temperature fluctuations and heat waves especially in the regions severely hit by climate change. Results The current study demonstrates the potential of beneficial bacteria for inducing heat tolerance in maize during early growth. Three Bacillus spp . AH-08, AH-67, SH-16, and one Pseudomonas spp . SH-29 showed the ability to grow and exhibited multiple plant-beneficial traits up to 45 ± 2 °C. At temperatures of 45 and 50 °C, Bacillus sp. SH-16 exhibited upregulation of two small heat shock proteins (HSP) of 15 and 30 kDa, while SH-16 and AH-67 showed upregulation of two large HSP of 65 and 100 kDa. Plant-inoculation with the consortium B3P (3 Bacillus + 1 Pseudomonas spp.) was carried out on six hybrid maize varieties pre-grown at 25 ± 2 ºC. Heat shock was applied to 10-day-old seedlings as: 3 h at 38ºC, 48 h recovery period, and then 48 h at 42ºC. The B3P treatment showed significant improvement in the overall plant growth (plant height, root & shoot fresh & dry weight, root and leaf area) with a higher level of CAT, POD, total chlorophyll, and carotenoids, while low concentration of MDA. A non-significant difference was observed in case of total cell protein and amino acids after B3P-treatment under stress. The expression of HSP1 and HSP18 in Malka and YH-5427 while HSP70 and HSP101 were higher in FH-1046 and Gohar as compared to non-inoculated treatment. Conclusions These findings indicate that heat-tolerant plant-growth promoting rhizobacteria (Ht-PGPR) exert versatile, multiphasic and differential response to improve plant growth and heat-tolerance in different maize varieties during seedling/ early vegetative growth. Subsequent research will be focused on the field evaluation of these PGPR to see the field and yield response of this consortium under natural temperature fluctuations in field.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135342806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Purpose As an invasive plant, Parthenium hysterophorus severely impacts the ecological environment of the Yellow River Delta and reduces biodiversity in the invaded areas. The effects of P. hysterophorus invasion on the local environment became increasingly critical, while few information was available for the effects of P. hysterophorus invasion on soil bacteria. The present study aimed to reveal the impacts of hysterophorus on the fungal communities in the Yellow River Delta. Methods Sixteen soil samples including four groups (ROOT group, YRR group, YNR group, and GBS group) were collected. High-throughput methods were used to explore the fungal composition of the P. hysterophorus -invaded surrounding environment and native plant-growed environment. Results Our results showed that the ACE (351.97) and Chao1 (351.95) values of the rhizosphere soils of P. hysterophorus (YRR group) were the highest among the four groups, whereas the non-rhizosphere soil samples of P. hysterophorus (YNR group) had the highest Shannon (7.188) and Simpson (0.984) values. The total number of operational taxonomic units (OTUs) obtained from the four groups was 1965, with 161 common OTUs among different groups. At the phylum level, both Ascomycota and Basidiomycota were the dominant fungi, with Ascomycota having the highest abundance. At the genus level, except for the endophytic fungi of P. hysterophorus roots (ROOT group), Fusarium , Mortierella , Comoclathris , and Cladosporium were the dominant fungi in three groups. The fungal communities within the roots of P. hysterophorus were distant from other groups, indicating that the composition of the fungal communities within the roots had a low degree of similarity to the other three groups. LEfSe analysis showed that Ascomycota at the phylum level and Cladosporium , Curvularia , and Alternaria at the genus level play essential roles in the ROOT group, and Comoclathris plays a vital role in the YNR group. Conclusions This study explored the effects of P. hysterophorus invasion on the local soil fungal communities by analyzing the fungal communities in P. hysterophorus roots , rhizosphere soil, non-rhizosphere soil, and rhizosphere soil of native plants. Generally, P. hysterophorus rhizosphere fungi specifically affect the surrounding environment.
{"title":"Impact of Parthenium hysterophorus L. invasion on soil fungal communities in the Yellow River Delta","authors":"Lixin Gong, Xin Xin, Wei Song, Zaiwang Zhang, Jiabo Zhang, Shuai Shang","doi":"10.1186/s13213-023-01735-6","DOIUrl":"https://doi.org/10.1186/s13213-023-01735-6","url":null,"abstract":"Abstract Purpose As an invasive plant, Parthenium hysterophorus severely impacts the ecological environment of the Yellow River Delta and reduces biodiversity in the invaded areas. The effects of P. hysterophorus invasion on the local environment became increasingly critical, while few information was available for the effects of P. hysterophorus invasion on soil bacteria. The present study aimed to reveal the impacts of hysterophorus on the fungal communities in the Yellow River Delta. Methods Sixteen soil samples including four groups (ROOT group, YRR group, YNR group, and GBS group) were collected. High-throughput methods were used to explore the fungal composition of the P. hysterophorus -invaded surrounding environment and native plant-growed environment. Results Our results showed that the ACE (351.97) and Chao1 (351.95) values of the rhizosphere soils of P. hysterophorus (YRR group) were the highest among the four groups, whereas the non-rhizosphere soil samples of P. hysterophorus (YNR group) had the highest Shannon (7.188) and Simpson (0.984) values. The total number of operational taxonomic units (OTUs) obtained from the four groups was 1965, with 161 common OTUs among different groups. At the phylum level, both Ascomycota and Basidiomycota were the dominant fungi, with Ascomycota having the highest abundance. At the genus level, except for the endophytic fungi of P. hysterophorus roots (ROOT group), Fusarium , Mortierella , Comoclathris , and Cladosporium were the dominant fungi in three groups. The fungal communities within the roots of P. hysterophorus were distant from other groups, indicating that the composition of the fungal communities within the roots had a low degree of similarity to the other three groups. LEfSe analysis showed that Ascomycota at the phylum level and Cladosporium , Curvularia , and Alternaria at the genus level play essential roles in the ROOT group, and Comoclathris plays a vital role in the YNR group. Conclusions This study explored the effects of P. hysterophorus invasion on the local soil fungal communities by analyzing the fungal communities in P. hysterophorus roots , rhizosphere soil, non-rhizosphere soil, and rhizosphere soil of native plants. Generally, P. hysterophorus rhizosphere fungi specifically affect the surrounding environment.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136308717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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