AIMS MicrobiologyPub Date : 2024-09-29eCollection Date: 2024-01-01DOI: 10.3934/microbiol.2024036
Afia Anjum, Jarin Tabassum, Sohidul Islam, A K M Imrul Hassan, Ishrat Jabeen, Sabbir R Shuvo
{"title":"Deciphering the genomic character of the multidrug-resistant <i>Staphylococcus aureus</i> from Dhaka, Bangladesh.","authors":"Afia Anjum, Jarin Tabassum, Sohidul Islam, A K M Imrul Hassan, Ishrat Jabeen, Sabbir R Shuvo","doi":"10.3934/microbiol.2024036","DOIUrl":"10.3934/microbiol.2024036","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> is one of the leading agents of nosocomial and community-acquired infections. In this study, we explored the genomic characterization of eight methicillin-resistant clinical isolates of <i>S. aureus</i> from Dhaka, Bangladesh. Notably, all strains were resistant to penicillin, cephalosporins, and monobactams, with partial susceptibility to meropenem and complete susceptibility to amikacin, vancomycin, and tigecycline antibiotics. The strains were found to have an average genome size of 2.73 Mbp and an average of 32.64% GC content. Multi-locus sequence typing analysis characterized the most predominant sequence type as ST361, which belongs to the clonal complex CC361. All isolates harbored the <i>mecA</i> gene, often linked to SCC<i>mec</i>_type IV variants. Multidrug resistance was attributed to efflux pumps NorA, NorC, SdrM, and LmrS alongside genes encoding beta-lactamase BlaZ and factors like ErmC and MepA. Additionally, virulence factors including <i>adsA</i>, <i>sdrC</i>, <i>cap8D</i>, <i>harA</i>, <i>esaA</i>, essC, <i>isdB</i>, <i>geh</i>, and <i>lip</i> were commonly identified. Furthermore, genes associated with heme uptake and clumping were present, highlighting their roles in <i>S. aureus</i> colonization and pathogenesis. Nine secondary metabolite biosynthetic gene clusters were found, of which six were common in all the strains. Numerous toxin-antitoxin systems were predicted, with ParE and ParB-like nuclease domains found to be the most prevalent toxin and antitoxin, respectively. Pan-genome analysis revealed 2007 core genes and 229 unique genes in the studied strains. Finally, the phylogenomic analysis showed that most Bangladeshi strains were grouped into two unique clades. This study provides a genomic and comparative insight into the multidrug resistance and pathogenicity of <i>S. aureus</i> strains, which will play a crucial role in the future antibiotic stewardship of Bangladesh.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"10 4","pages":"833-858"},"PeriodicalIF":2.7,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11609420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142773473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AIMS MicrobiologyPub Date : 2024-09-24eCollection Date: 2024-01-01DOI: 10.3934/microbiol.2024035
Chunze Zhang, Mingqian Ma, Zhenying Zhao, Zhiqiang Feng, Tianhao Chu, Yijia Wang, Jun Liu, Xuehua Wan
{"title":"Gut mucosal microbiota profiles linked to development of positional-specific human colorectal cancer.","authors":"Chunze Zhang, Mingqian Ma, Zhenying Zhao, Zhiqiang Feng, Tianhao Chu, Yijia Wang, Jun Liu, Xuehua Wan","doi":"10.3934/microbiol.2024035","DOIUrl":"10.3934/microbiol.2024035","url":null,"abstract":"<p><p>Colorectal cancer (CRC) continuously ranks as the third most common cause of cancer-related deaths worldwide. Based on anatomical classifications and clinical diagnoses, CRC is classified into right-sided, left-sided, and rectal CRC. Importantly, the three types of positional-specific CRC affect the prognosis outcomes, thus indicating that positional-specific treatments for CRC are required. Emerging evidence suggests that besides host genetic and epigenetic alterations, gut mucosal microbiota is linked to gut inflammation, CRC occurrence, and prognoses. However, gut mucosal microbiota associated with positional-specific CRC are poorly investigated. Here, we report the gut mucosal microbiota profiles associated with these three types of CRC. Our analysis showed that the unique composition and biodiversity of bacterial taxa are linked to positional-specific CRC. We found that a combination of bacterial taxa can serve as potential biomarkers to distinguish the three types of CRC. Further investigations of the physiological roles of bacteria associated with positional-specific CRC may help understand the mechanism of CRC progression in different anatomical locations under the impact of gut mucosal microbiota.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"10 4","pages":"812-832"},"PeriodicalIF":2.7,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11609426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142773488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Antioxidant and anti-inflammatory properties of water kefir microbiota and its bioactive metabolites for health promoting bio-functional products and applications.","authors":"Dimitra Papadopoulou, Vasiliki Chrysikopoulou, Aikaterini Rampaouni, Alexandros Tsoupras","doi":"10.3934/microbiol.2024034","DOIUrl":"10.3934/microbiol.2024034","url":null,"abstract":"<p><p>Inflammation and oxidative stress are implicated in several chronic disorders, while healthy foods and especially fermented beverages and those containing probiotics can provide anti-inflammatory and antioxidant protection against such manifestations and the associated disorders. Water kefir is such a beverage that is rich in both probiotic microbiota and anti-inflammatory bioactives, with an increasing demand as an alternative to a fermented product based on non-dairy matrix with potential health properties. Within this study, the health-promoting properties of the most representative species and strains of microorganisms present in water kefir grains, as well as the health benefits attributed to the bioactive metabolites produced by each individual strain in a series of their cultures, were thoroughly reviewed. Emphasis was given to the antioxidant, antithrombotic, and anti-inflammatory bio-functionalities of both the cultured microorganisms and the bioactive metabolites produced in each case. Moreover, an extensive presentation of the antioxidant and anti-inflammatory health benefits observed from the overall water kefir cultures and classic water kefir beverages obtained were also conducted. Finally, the use of water kefir for the production of several other bio-functional products, including fermented functional foods, supplements, nutraceuticals, nutricosmetics, cosmeceuticals, and cosmetic applications with anti-inflammatory and antioxidant health promoting potential was also thoroughly discussed. Limitations and future perspectives on the use of water kefir, its microorganisms, and their bioactive metabolites are also outlined.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"10 4","pages":"756-811"},"PeriodicalIF":2.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11609422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142773396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AIMS MicrobiologyPub Date : 2024-08-23eCollection Date: 2024-01-01DOI: 10.3934/microbiol.2024033
Giuseppe Maglione, Paola Zinno, Alessia Tropea, Cassamo U Mussagy, Laurent Dufossé, Daniele Giuffrida, Alice Mondello
{"title":"Microbes' role in environmental pollution and remediation: a bioeconomy focus approach.","authors":"Giuseppe Maglione, Paola Zinno, Alessia Tropea, Cassamo U Mussagy, Laurent Dufossé, Daniele Giuffrida, Alice Mondello","doi":"10.3934/microbiol.2024033","DOIUrl":"10.3934/microbiol.2024033","url":null,"abstract":"<p><p>Bioremediation stands as a promising solution amid the escalating challenges posed by environmental pollution. Over the past 25 years, the influx of synthetic chemicals and hazardous contaminants into ecosystems has required innovative approaches for mitigation and restoration. The resilience of these compounds stems from their non-natural existence, distressing both human and environmental health. Microbes take center stage in this scenario, demonstrating their ability of biodegradation to catalyze environmental remediation. Currently, the scientific community supports a straight connection between biorefinery and bioremediation concepts to encourage circular bio/economy practices. This review aimed to give a pre-overview of the state of the art regarding the main microorganisms employed in bioremediation processes and the different bioremediation approaches applied. Moreover, focus has been given to the implementation of bioremediation as a novel approach to agro-industrial waste management, highlighting how it is possible to reduce environmental pollution while still obtaining value-added products with commercial value, meeting the goals of a circular bioeconomy. The main drawbacks and challenges regarding the feasibility of bioremediation were also reported.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"10 3","pages":"723-755"},"PeriodicalIF":2.7,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142116995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AIMS MicrobiologyPub Date : 2024-08-22eCollection Date: 2024-01-01DOI: 10.3934/microbiol.2024032
Anna-Maria Gierke, Petra Vatter, Martin Hessling
{"title":"Fungal photoinactivation doses for UV radiation and visible light-a data collection.","authors":"Anna-Maria Gierke, Petra Vatter, Martin Hessling","doi":"10.3934/microbiol.2024032","DOIUrl":"10.3934/microbiol.2024032","url":null,"abstract":"<p><p>Nearly two million people die each year from fungal infections. Additionally, fungal crop infections jeopardize the global food supply. The use of 254 nm UVC radiation from mercury vapor lamps is a disinfection technique known to be effective against all microorganisms, and there are surveys of published UVC sensitivities. However, these mainly focus on bacteria and viruses. Therefore, a corresponding overview for fungi will be provided here, including far-UVC, UVB, UVA, and visible light, in addition to the conventional 254 nm UVC inactivation. The available literature was searched for photoinactivation data for fungi in the above-mentioned spectral ranges. To standardize the presentation, the mean log-reduction doses were retrieved and sorted by fungal species, spectral range, wavelength, and medium, among others. Additionally, the median log-reduction dose was determined for fungi in transparent liquid media. Approximately 400 evaluable individual data sets from publications over the last 100 years were compiled. Most studies were performed with 254 nm radiation from mercury vapor lamps on <i>Aspergillus niger</i>, <i>Candida albicans</i>, and <i>Saccharomyces cerevisiae</i>. However, the data found were highly scattered, which could be due to the experimental conditions. Even though the number of individual data sets seems large, many important fungi have not been extensively studied so far. For example, UV irradiation data does not yet exist for half of the fungal species classified as \"high priority\" or \"medium priority\" by the World Health Organization (WHO). In addition, researchers should measure the transmission of their fungal suspensions at the irradiation wavelength to avoid the undesirable effects of either absorption or scattering on irradiation results.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"10 3","pages":"694-722"},"PeriodicalIF":2.7,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AIMS MicrobiologyPub Date : 2024-08-21eCollection Date: 2024-01-01DOI: 10.3934/microbiol.2024031
Mohammad Zahangeer Alam, Malancha Dey Roy
{"title":"The reduction of abiotic stress in food crops through climate-smart mycorrhiza-enriched biofertilizer.","authors":"Mohammad Zahangeer Alam, Malancha Dey Roy","doi":"10.3934/microbiol.2024031","DOIUrl":"10.3934/microbiol.2024031","url":null,"abstract":"<p><p>Climate change enhances stress in food crops. Recently, abiotic stress such as metalloid toxicity, salinity, and drought have increased in food crops. Mycorrhizal fungi can accumulate several nutrients within their hyphae through a symbiotic relationship and release them to cells in the root of the food crops under stress conditions. We have studied arbuscular mycorrhizal fungi (AMF)-enriched biofertilizers as a climate-smart technology option to increase safe and healthy food production under abiotic stress. AMF such as <i>Glomus sp</i>., <i>Rhizophagus sp</i>., <i>Acaulospora morrowiae</i>, <i>Paraglomus occultum</i>, <i>Funneliformis mosseae</i>, and <i>Claroideoglomus etunicatum</i> enhance growth and yield in food crops grown in soils under abiotic stress. AMF also works as a bioremediation material in food crops grown in soil. More precisely, the arsenic concentrations in grains decrease by 57% with AMF application. In addition, AMF increases mineral contents, and antioxidant activities under drought and salinity stress in food crops. Catalase (CAT) and ascorbate peroxidase (APX) increased by 45% and 70% in AMF-treated plants under drought stress. AMF-enriched biofertilizers are used in crop fields like precision agriculture to reduce the demand for chemical fertilizers. Subsequently, AMF-enriched climate-smart biofertilizers increase nutritional quality by reducing abiotic stress in food crops grown in soils. Consequently, a climate resilience environment might be developed using AMF-enriched biofertilizers for sustainable livelihood.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"10 3","pages":"674-693"},"PeriodicalIF":2.7,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362269/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AIMS MicrobiologyPub Date : 2024-08-08eCollection Date: 2024-01-01DOI: 10.3934/microbiol.2024030
Jasenka Sremac, Marija Bošnjak, Karmen Fio Firi, Ana Šimičević, Šimun Aščić
{"title":"Marine microfossils: Tiny archives of ocean changes through deep time.","authors":"Jasenka Sremac, Marija Bošnjak, Karmen Fio Firi, Ana Šimičević, Šimun Aščić","doi":"10.3934/microbiol.2024030","DOIUrl":"10.3934/microbiol.2024030","url":null,"abstract":"<p><p>Microorganisms have inhabited the oceans since the dawn of Earth. Some of them have organic walls and some produce mineral tests that are usually composed of carbonate minerals or silica. They can therefore be preserved with original parts during sedimentary deposition or fossilized through permineralization or carbonization processes. The most common marine fossil groups studied by micropaleontologists are cyanobacteria, coccolithophores, dinoflagellates, diatoms, silicoflagellates, radiolarians, foraminifers, red and green algae, ostracods, and pteropods. Dormant or reproductive cysts can also be used for determinations of the fossil microbiota. Microfossils can be studied in petrographic slides prepared from rocks or separated from loosely consolidated rocks by disaggregation or dissolution and wet sieving. Their presence is sometimes recognized by biomarkers. Transmitted light microscopy and reflected light stereomicroscopy are necessary for micropaleontological studies whereas scanning electronic microscopy (SEM) aids research on the tiniest fossils and reveals fine skeletal details. Microorganisms have influenced the oxygenation of water and the atmosphere, as well as Earth's carbon cycle and have contributed to the formation of sedimentary rocks. By studying microfossils, paleontologists depict the age of the rock and identify depositional environments. Such studies help us recognize periods of stress in Earth's history and understand their influence on living organisms. Biogenic rocks, made of microfossils, can be used as raw materials, such as fossil fuels, building stone, or additives for the food industry, agricultural, or cosmetic purposes.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"10 3","pages":"644-673"},"PeriodicalIF":2.7,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AIMS MicrobiologyPub Date : 2024-08-07eCollection Date: 2024-01-01DOI: 10.3934/microbiol.2024029
Karlene Lambrechts, Pieter Gouws, Diane Rip
{"title":"Genetic diversity of <i>Listeria monocytogenes</i> from seafood products, its processing environment, and clinical origin in the Western Cape, South Africa using whole genome sequencing.","authors":"Karlene Lambrechts, Pieter Gouws, Diane Rip","doi":"10.3934/microbiol.2024029","DOIUrl":"10.3934/microbiol.2024029","url":null,"abstract":"<p><p><i>Listeria monocytogenes</i> is a concern in seafood and its food processing environment (FPE). Several outbreaks globally have been linked to various types of seafood. Genetic profiling of <i>L. monocytogenes</i> is valuable to track bacterial contamination throughout the FPE and in understanding persistence mechanisms, with limited studies from South Africa. Forty-six <i>L. monocytogenes</i> isolates from origins: Fish/seafood products (n = 32) (salmon, smoked trout, fresh hake, oysters), the FPE (n = 6), and clinical (n = 8) were included in this study. Lineage typing, antibiotic susceptibility testing, and screening for two genes (<i>bcrABC</i> and <i>emrC</i>) conferring sanitizer tolerance was conducted. The seafood and FPE isolates originated from seven different factories processing various seafood products with undetermined origin. All clinical isolates were categorized as lineage I, and seafood and FPE isolates were mostly categorized into lineage II (p < 0.01). Seafood and FPE isolates (53%) carried the <i>bcrABC</i> gene cassette and one fish isolate, the <i>emrC</i> gene. A subset, n = 24, was grouped into serotypes, sequence types (STs), and clonal complexes (CCs) with whole genome sequencing (WGS). Eight CCs and ten STs were identified. All clinical isolates belonged to serogroup 4b, hypervirulent CC1. CC121 was the most prevalent in isolates from food and the FPE. All isolates carried <i>Listeria</i> pathogenicity islands (LIPI) 1 and 2. LIPI-3 and LIPI-4 were found in certain isolates. We identified genetic determinants linked to enhanced survival in the FPE, including stress survival islets (SSI) and genes conferring tolerance to sanitizers. SSI-1 was found in 44% isolates from seafood and the FPE. SSI-2 was found in all the ST121 seafood isolates. Isolates (42%) harbored transposon Tn1688_qac (<i>ermC</i>), conferring tolerance to quaternary ammonium compounds. Five plasmids were identified in 13 isolates from seafood and the FPE. This is the first One Health study reporting on <i>L. monocytogenes</i> genetic diversity, virulence and resistance profiles from various types of seafood and its FPE in South Africa.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"10 3","pages":"608-643"},"PeriodicalIF":2.7,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AIMS MicrobiologyPub Date : 2024-07-30eCollection Date: 2024-01-01DOI: 10.3934/microbiol.2024028
Marzieh Sajadi Bami, Payam Khazaeli, Shayan Fakhraei Lahiji, Gholamreza Dehghannoudeh, Ibrahim M Banat, Mandana Ohadi
{"title":"Potential of biosurfactant as green pharmaceutical excipients for coating of microneedles: A mini review.","authors":"Marzieh Sajadi Bami, Payam Khazaeli, Shayan Fakhraei Lahiji, Gholamreza Dehghannoudeh, Ibrahim M Banat, Mandana Ohadi","doi":"10.3934/microbiol.2024028","DOIUrl":"10.3934/microbiol.2024028","url":null,"abstract":"<p><p>Microneedles, a novel transdermal delivery system, were designed to improve drug delivery and address the challenges typically encountered with traditional injection practices. Discovering new and safe excipients for microneedle coating to replace existing chemical surfactants is advantageous to minimize their side effect on viable tissues. However, some side effects have also been observed for this application. The vast majority of studies suggest that using synthetic surfactants in microneedle formulations may result in skin irritation among other adverse effects. Hence, increasing knowledge about these components and their potential impacts on skin paves the way for finding preventive strategies to improve their application safety and potential efficacy. Biosurfactants, which are naturally produced surface active microbial products, are proposed as an alternative to synthetic surfactants with reduced side effects. The current review sheds light on potential and regulatory aspects of biosurfactants as safe excipients in the coating of microneedles.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"10 3","pages":"596-607"},"PeriodicalIF":2.7,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
AIMS MicrobiologyPub Date : 2024-07-23eCollection Date: 2024-01-01DOI: 10.3934/microbiol.2024027
William D Eaton, Debra A Hamilton, Wen Chen, Alexander Lemenze, Patricia Soteropoulos
{"title":"Use of high throughput DNA analysis to characterize the nodule-associated bacterial community from four ages of <i>Inga punctata</i> trees in a Costa Rican cloud forest.","authors":"William D Eaton, Debra A Hamilton, Wen Chen, Alexander Lemenze, Patricia Soteropoulos","doi":"10.3934/microbiol.2024027","DOIUrl":"10.3934/microbiol.2024027","url":null,"abstract":"<p><p>Leguminous tree root nodule nitrogen-fixing bacteria are critical for recuperation of soil C and N cycle processes after disturbance in tropical forests, while other nodule-associated bacteria (NAB) may enhance nodule development and activity, and plant growth. However, little is known of these root nodule microbiomes. Through DNA analysis, we evaluated the bacterial taxa associated with the root nodules of the 1-year-old, 2-year-old, 13-year-old, and old growth <i>Inga punctata</i> trees in a cloud forest. <i>Bradyrhizobium diazoefficiens</i> was the dominant taxon found in all nodules at 63.16% to 85.71% mean percent sequences (MPS) of the total nodule bacterial DNA and was found in the youngest nodules examined (1 year old), suggesting that it is the primary nodular bacteria. There were 26 other NAB genera with collective MPS levels between 7.4% to 12.2%, while 15 of these genera were found in the Bulk Forest soils at collective MPS levels of 4.6%. These bacterial community compositions were different between the NAB and Bulk Forest soils, suggesting the NAB became concentrated within the root nodules, resulting in communities with different compositions from the Bulk Forest soils. Twenty-three of the 26 NAB genera were previously identified with the potential to perform 9 plant growth promoting (PGP) activities, suggesting their importance in root nodule development and plant growth. These NAB communities appeared to successionally develop over time into more complex taxonomic communities, which is consistent with the outcome of advanced microbial communities following succession. The presence of both <i>B. diazoefficiens</i> and the NAB communities in the nodules across all ages of tree roots, and the potential for PGP activities linked with most of the NAB genera, suggest the importance of <i>B. diazoefficiens</i> and the NAB community for nodule development and enhanced development and growth of <i>I. punctata</i> throughout its lifespan, and most critically in the younger plants.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"10 3","pages":"572-595"},"PeriodicalIF":2.7,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}