Microbial communities from arid environments on a global scale. A systematic review

AbstractA demand-driven approach is becoming increasingly central in the efforts to improve agricultural research and development. However, the question of how exactly demand is studied usually remains unstated and is rarely discussed. We therefore carried out a systematic review in order to better understand how farmers’ demand for seed in root, tuber and banana seed systems is studied. The review is based on data from a consultation with an expert panel and a structured literature search in the SCOPUS database. Screening the gathered articles resulted in 46 studies on a global scale, fitting the scope of our investigation. Through qualitative analysis and categorization of these studies, we developed a classification scheme according to the types of approaches applied in the retained studies. One group of studies explicitly articulates farmers’ preferences and choices through surveys or engagements in trials, auctions, choice experiments and interviews. Other studies implicitly articulate farmers’ demand by characterising their current use of varieties and seed. We discuss opportunities and limitations in the use of each type of study and we reflect on the body of available literature as a whole. Our conclusion is that a framework is necessary that purposefully combines the existing different methods and that it is necessary to involve stakeholders in a process where demand is articulated. Together, these two steps would characterise existing demands in a more effective and precise way, thus providing better guidance to decision-makers in their reactions pertaining to seed systems.

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Significant Changes in Microbial Communities Associated With Reef Corals in the Southern South China Sea During the 2015/2016 Global‐Scale Coral Bleaching Event

Journal of Geophysical Research Oceans ◽

10.1029/2019jc015579 ◽

2020 ◽

Vol 125 (7) ◽

Author(s):

Zhenjun Qin ◽

Kefu Yu ◽

Jiayuan Liang ◽

Qiucui Yao ◽

Biao Chen

Keyword(s):

South China Sea ◽

Microbial Communities ◽

South China ◽

Coral Bleaching ◽

Global Scale ◽

Bleaching Event ◽

Southern South China Sea ◽

Reef Corals ◽

China Sea

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β-Glucosidase genes differentially expressed during composting

Biotechnology for Biofuels ◽

10.1186/s13068-020-01813-w ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Xinyue Zhang ◽

Bo Ma ◽

Jiawen Liu ◽

Xiehui Chen ◽

Shanshan Li ◽

...

Keyword(s):

Microbial Communities ◽

Environmental Changes ◽

Cellulose Degradation ◽

Degradation Mechanism ◽

Degradation Process ◽

Global Scale ◽

Expression Of Genes ◽

Glucose Tolerant ◽

Cooling Phase ◽

And Function

Abstract Background Cellulose degradation by cellulase is brought about by complex communities of interacting microorganisms, which significantly contribute to the cycling of carbon on a global scale. β-Glucosidase (BGL) is the rate-limiting enzyme in the cellulose degradation process. Thus, analyzing the expression of genes involved in cellulose degradation and regulation of BGL gene expression during composting will improve the understanding of the cellulose degradation mechanism. Based on our previous research, we hypothesized that BGL-producing microbial communities differentially regulate the expression of glucose-tolerant BGL and non-glucose-tolerant BGL to adapt to the changes in cellulose degradation conditions. Results To confirm this hypothesis, the structure and function of functional microbial communities involved in cellulose degradation were investigated by metatranscriptomics and a DNA library search of the GH1 family of BGLs involved in natural and inoculated composting. Under normal conditions, the group of non-glucose-tolerant BGL genes exhibited higher sensitivity to regulation than the glucose-tolerant BGL genes, which was suppressed during the composting process. Compared with the expression of endoglucanase and exoglucanase, the functional microbial communities exhibited a different transcriptional regulation of BGL genes during the cooling phase of natural composting. BGL-producing microbial communities upregulated the expression of glucose-tolerant BGL under carbon catabolite repression due to the increased glucose concentration, whereas the expression of non-glucose-tolerant BGL was suppressed. Conclusion Our results support the hypothesis that the functional microbial communities use multiple strategies of varying effectiveness to regulate the expression of BGL genes to facilitate adaptation to environmental changes.

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Comparative Study of the Rhizosphere and Root Endosphere Microbiomes of Cholistan Desert Plants

Frontiers in Microbiology ◽

10.3389/fmicb.2021.618742 ◽

2021 ◽

Vol 12 ◽

Author(s):

Salma Mukhtar ◽

Samina Mehnaz ◽

Kauser Abdulla Malik

Keyword(s):

Microbial Diversity ◽

Microbial Communities ◽

Arid Regions ◽

Soil Moisture Content ◽

Abiotic Factors ◽

Arid Environments ◽

Desert Plants ◽

Limited Information ◽

Cholistan Desert ◽

Capparis Decidua

Microbial communities associated with the rhizosphere and roots of desert halophytes play an important role in plants’ growth and development. Very limited information has been available on the microbial diversity of arid environments of Pakistan. Hence in the current study, the microbial diversity of rhizosphere and root endosphere of desert halophytes, Zygophyllum simplex, Haloxylon salicoricum, Aerva javanica, and Capparis decidua was evaluated. The rhizosphere and root endosphere samples of desert halophytes collected from the three geographic sites of Cholistan desert, Punjab, Pakistan were analyzed by using 16S rRNA based Illumina sequencing. The results showed that Proteobacteria were more abundant in the rhizospheric soils while Actinobacteria were more dominant in the root endosphere of halophytes. Bacteroidetes, Firmicutes, and Deinococcus-Thermus were identified from all rhizospheric soils and roots across the three sites, with variable percentage. Bacillus, Kocuria, Pseudomonas, Halomonas, and Flavobacterium were commonly identified from the rhizosphere and root endosphere of halophytes across all the three sites. At the genus level, microbial diversity from Haloxylon showed the greatest variations between the rhizosphere and root endosphere from the site 2. This study revealed that microbial diversity analysis can be used to study how changes in abiotic factors such as soil moisture content and salinity affect the microbial communities associated with the rhizospheric soils and root endosphere of halophytes across the three sites. This study will also help in the discovery of potential inoculants for crops growing in arid and semi-arid regions of Pakistan.

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An ecophysiological explanation for manganese enrichment in rock varnish

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2025188118 ◽

2021 ◽

Vol 118 (25) ◽

pp. e2025188118

Author(s):

Usha F. Lingappa ◽

Chris M. Yeager ◽

Ajay Sharma ◽

Nina L. Lanza ◽

Demosthenes P. Morales ◽

...

Keyword(s):

Microbial Communities ◽

Imaging Techniques ◽

Manganese Content ◽

Chemical Imaging ◽

Arid Environments ◽

Metagenomic Dna ◽

Paramagnetic Resonance ◽

Desert Varnish ◽

Specific Uptake ◽

Petrographic Thin Section

Desert varnish is a dark rock coating that forms in arid environments worldwide. It is highly and selectively enriched in manganese, the mechanism for which has been a long-standing geological mystery. We collected varnish samples from diverse sites across the western United States, examined them in petrographic thin section using microscale chemical imaging techniques, and investigated the associated microbial communities using 16S amplicon and shotgun metagenomic DNA sequencing. Our analyses described a material governed by sunlight, water, and manganese redox cycling that hosts an unusually aerobic microbial ecosystem characterized by a remarkable abundance of photosynthetic Cyanobacteria in the genus Chroococcidiopsis as the major autotrophic constituent. We then showed that diverse Cyanobacteria, including the relevant Chroococcidiopsis taxon, accumulate extraordinary amounts of intracellular manganese—over two orders of magnitude higher manganese content than other cells. The speciation of this manganese determined by advanced paramagnetic resonance techniques suggested that the Cyanobacteria use it as a catalytic antioxidant—a valuable adaptation for coping with the substantial oxidative stress present in this environment. Taken together, these results indicated that the manganese enrichment in varnish is related to its specific uptake and use by likely founding members of varnish microbial communities.

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The global molecular epidemiology of microsporidia infection in sheep and goats with focus on Enterocytozoon bieneusi: a systematic review and meta-analysis

Tropical Medicine and Health ◽

10.1186/s41182-021-00355-7 ◽

2021 ◽

Vol 49 (1) ◽

Author(s):

Ali Taghipour ◽

Saeed Bahadory ◽

Ehsan Javanmard

Keyword(s):

Systematic Review ◽

Meta Analysis ◽

Small Ruminants ◽

Global Scale ◽

Enterocytozoon Bieneusi ◽

Control Measures ◽

Sheep And Goats ◽

Prevalence Studies ◽

Global Estimate ◽

Meta Analyses

Abstract Background Microsporidia is a zoonotic pathogen with health consequences in immunocompromised patients. Small ruminants are a potential reservoir of microsporidia for humans in their vicinity. Hence, we aimed to evaluate the molecular prevalence of microsporidian infections with emphasis on Enterocytozoon bieneusi genotypes among sheep and goats at a global scale through systematic review and meta-analysis approach. Methods The standard protocol of preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were followed. Eligible prevalence studies on small ruminant microsporidiosis, published from 1 January 2000 until 15 April 2021 were gathered using systematic literature search in PubMed, Scopus, Web of Science and Google Scholar databases. Inclusion and exclusion criteria were applied. The point estimates and 95% confidence intervals were calculated using a random-effects model. The variance between studies (heterogeneity) was quantified by I2 index. Results In total, 25 articles (including 34 datasets) were included for final meta-analysis. The pooled molecular prevalence of microsporidia in sheep and goats was estimated to be 17.4% (95% CI: 11.8–25%) and 16% (95% CI: 11.2–22.4%), respectively. Likewise, the overall prevalence of E. bieneusi was estimated to be 17.4% (95% CI: 11.8–25%) for sheep and 16.3% (95% CI: 11.3–22.8%) for goats. According to internal transcribed spacer (ITS) gene analysis, E. bieneusi with genotypes BEB6 (15 studies) and COS-1 (nine studies) in sheep, and CHG3 (six studies) and BEB6 (five studies) in goats were the highest reported genotypes. Conclusion The present results highlight the role of sheep and goats as reservoir hosts for human-infecting microsporidia. Therefore, this global estimate could be beneficial on preventive and control measures.

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Comorbidities in SARS-CoV-2 Patients: a Systematic Review and Meta-Analysis

mBio ◽

10.1128/mbio.03647-20 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Wern Hann Ng ◽

Thomas Tipih ◽

Nigel A. Makoah ◽

Jan-G Vermeulen ◽

Dominique Goedhals ◽

...

Keyword(s):

Diabetes Mellitus ◽

Systematic Review ◽

Kidney Diseases ◽

Meta Analysis ◽

Risk Groups ◽

Global Scale ◽

Obesity And Diabetes ◽

Study Selection ◽

The Status ◽

Using Data

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread across the globe at unprecedented speed and is showing no signs of slowing down. The outbreak of coronavirus disease 2019 (COVID-19) has led to significant health burden in infected patients especially in those with underlying comorbidities. The aim of this study was to evaluate the correlation between comorbidities and their role in the exacerbation of disease in COVID-19 patients leading to fatal outcomes. A systematic review was conducted using data from MEDLINE, Scopus, Web of Science, and EMBASE databases published from 1 December 2019 to 15 September 2020. Fifty-three articles were included in the systematic review. Of those 53 articles, 8 articles were eligible for meta-analysis. Hypertension, obesity, and diabetes mellitus were identified to be the most prevalent comorbidities in COVID-19 patients. Our meta-analysis showed that cancer, chronic kidney diseases, diabetes mellitus, and hypertension were independently associated with mortality in COVID-19 patients. Chronic kidney disease was statistically the most prominent comorbidity leading to death. However, despite having high prevalence, obesity was not associated with mortality in COVID-19 patients. IMPORTANCE COVID-19 has plagued the world since it was first identified in December 2019. Previous systematic reviews and meta-analysis were limited by various factors such as the usage of non-peer reviewed data and were also limited by the lack of clinical data on a global scale. Comorbidities are frequently cited as risk factors for severe COVID-19 outcomes. However, the degree to which specific comorbidities impact the disease is debatable. Our study selection involves a global reach and covers all comorbidities that were reported to be involved in the exacerbation of COVID-19 leading to fatal outcomes, which allows us to identify the specific comorbidities that have higher risk in patients. The study highlights COVID-19 high-risk groups. However, further research should focus on the status of comorbidities and prognosis in COVID-19 patients.

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The mystery of COVID-19 reinfections: A global systematic review and meta-analysis of 577 cases

10.1101/2021.07.22.21260972 ◽

2021 ◽

Author(s):

Rubaid Azhar Dhillon ◽

Mohammad Aadil Qamar ◽

Omar Irfan ◽

Jaleed Ahmed Gilani ◽

Usama Waqar ◽

...

Keyword(s):

Systematic Review ◽

Assessment Tool ◽

Meta Analysis ◽

Case Series ◽

Admission Rate ◽

Global Scale ◽

Common Symptom ◽

Time Duration ◽

Disease Spectrum ◽

Meta Analyses

Background As the COVID-19 pandemic rages on, reports on disparities in vaccine roll out alongside reinfection and reactivation from previously recovered cases have been emerging. With newer waves and variants of COVID-19, we conducted a systematic review to assess the determinants and disease spectrum of COVID-19 reinfection. Methods A comprehensive search covering relevant databases was conducted for observational studies reporting Polymerase Chain Reaction (PCR) confirmed infection and reinfection cases. Quality assessment tool developed by the National Institute of Health (NIH) for assessment of case series was used. Meta-analyses were performed using RevMan 5.3 for pooled proportions of findings in first infection and reinfection with 95% confidence interval (CI). Results Eighty-one studies reporting 577 cases were included from 22 countries. The mean age of patients was 46.2±18.9 years with males accounting for 45.8% of the study population while 179 (31.0%) cases of comorbidities were reported. The average time duration between first infection and reinfection was 63.6±48.9 days. During first infection and reinfection, fever was the most common symptom (41.4% and 36.4%,respectively) whilst anti-viral therapy was the most common treatment regimen administered (44.5% and 43.0%, respectively). Overall, comparable odds of symptomatic presentation and management were reported in the two infections. However, a higher Intensive Care Unit (ICU) admission rate was observed in reinfection compared to first infection (10 vs 3). Ten deaths were reported with 565 patients fully recovering. Respiratory failure was the most common cause of death (7/10 deaths). Seventy-two studies were determined to be of good quality whilst nine studies were of fair quality. Conclusion As the first global-scale systematic review of its kind, our findings support immunization practices given increased ICU admissions and mortality in reinfections. Our cohort serves as a guide for clinicians and authorities for devising an optimal strategy for controlling the pandemic.

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Global-Scale Structure of the Eelgrass Microbiome

Applied and Environmental Microbiology ◽

10.1128/aem.03391-16 ◽

2017 ◽

Vol 83 (12) ◽

Cited By ~ 52

Author(s):

Ashkaan K. Fahimipour ◽

Melissa R. Kardish ◽

Jenna M. Lang ◽

Jessica L. Green ◽

Jonathan A. Eisen ◽

...

Keyword(s):

Microbial Communities ◽

Community Assembly ◽

Zostera Marina ◽

Spatial Scales ◽

Metabolic Modeling ◽

Global Scale ◽

Sampling Effort ◽

Content Type ◽

Terrestrial Species ◽

Root Surfaces

ABSTRACT Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. Here, we report the results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of surrounding seawater and sediment, we uncovered the structure, composition, and variability of microbial communities associated with eelgrass. We also investigated hypotheses about the assembly of the eelgrass microbiome using a metabolic modeling approach. Our results reveal leaf communities displaying high variability and spatial turnover that mirror their adjacent coastal seawater microbiomes. By contrast, roots showed relatively low compositional turnover and were distinct from surrounding sediment communities, a result driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Predictions from metabolic modeling of enriched taxa were consistent with a habitat-filtering community assembly mechanism whereby similarity in resource use drives taxonomic cooccurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a core eelgrass root microbiome with putative functional roles and highlights potentially disparate processes influencing microbial community assembly on different plant compartments. IMPORTANCE Plants depend critically on their associated microbiome, yet the structure of microbial communities found on marine plants remains poorly understood in comparison to that for terrestrial species. Seagrasses are the only flowering plants that live entirely in marine environments. The return of terrestrial seagrass ancestors to oceans is among the most extreme habitat shifts documented in plants, making them an ideal testbed for the study of microbial symbioses with plants that experience relatively harsh abiotic conditions. In this study, we report the results of a global sampling effort to extensively characterize the structure of microbial communities associated with the widespread seagrass species Zostera marina, or eelgrass, across its geographic range. Our results reveal major differences in the structure and composition of above- versus belowground microbial communities on eelgrass surfaces, as well as their relationships with the environment and host.

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