Microbiome signature and diversity regulates the level of energy production under anaerobic condition

Zeng

et al. 2021

Biology

To investigate the diversity and structure of soil bacterial and fungal communities in saline soils, soil samples with three increasing salinity levels (S1, S2 and S3) were collected from a maize field in Yanqi, Xinjiang Province, China. The results showed that the K+, Na+, Ca2+ and Mg2+ values in the bulk soil were higher than those in the rhizosphere soil, with significant differences in S2 and S3 (p < 0.05). The enzyme activities of alkaline phosphatase (ALP), invertase, urease and catalase (CAT) were lower in the bulk soil than those in the rhizosphere. Principal coordinate analysis (PCoA) demonstrated that the soil microbial community structure exhibited significant differences between different salinized soils (p < 0.001). Data implied that the fungi were more susceptible to salinity stress than the bacteria based on the Shannon and Chao1 indexes. Mantel tests identified Ca2+, available phosphorus (AP), saturated electrical conductivity (ECe) and available kalium (AK) as the dominant environmental factors correlated with bacterial community structures (p < 0.001); and AP, urease, Ca2+ and ECe as the dominant factors correlated with fungal community structures (p < 0.001). The relative abundances of Firmicutes and Bacteroidetes showed positive correlations with the salinity gradient. Our findings regarding the bacteria having positive correlations with the level of salinization might be a useful biological indicator of microorganisms in saline soils.

Section: Methodsmentioning

confidence: 99%

Responses of the Soil Microbial Community to Salinity Stress in Maize Fields

Zeng

et al. 2021

Biology

“…Different species of Saccharomycetales such as S. paradoxus, S. kudriavzevii, K. lactis, K. aquatica, Y. lipolytica had an opportunistic inclusion in COVID-19 patients (Fig 9, S1 Data). Earlier evidences suggested that different species Saccharomycetales can only perform opportunistic or passive crossings when epithelial barrier integrity of the NT is previously compromised by other infectious agents [70]. For instance, S. kudriavzevii an opportunistic pathogen especially potential hazard to the health of immunocompromised workers in the wine industry, and potentially also to consumers [61].…”

Section: Discussionmentioning

confidence: 99%

“…alignment length cut off: 20) [69]. The association between metabolic functions and dominant fungal species were measured using the Spearman’s correlation coefficient and significance tests [70]. The R packages, Hmisc (https://cran.r-project.org/web/packages/Hmisc/index.html) and corrplot (https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html) were used respectively to analyze and visualize the data.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Metagenomic analysis reveals the abundance and diversity of opportunistic fungal pathogens in the nasopharyngeal tract of COVID-19 patients

Hoque

Rahman²,

Sarkar

et al. 2022

Preprint

Self Cite

The nasopharyngeal tract (NT) of human is a habitat of a diverse microbial community that work together with other gut microbes to maintain the host immunity. In our previous study, we reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome (bacteria, archaea and commensal respiratory viruses) but increases the abundance of pathobionts. This study aimed to assess the possible changes in the resident fungal diversity by the inclusion of opportunistic fungi due to the infection of SARS-CoV-2 in the NT of humans. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNAseq-based metagenomics analyses. Our results indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of NT fungi with a high inclusion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct microbiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where Saccharomyces cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species in the NT of COVID-19 patients. Importantly, 16% commensal fungal species found in the Healthy control were not detected in either COVID-19 patients or when they were recovered from the COVID-19. Pairwise Spearman's correlation test showed that several altered metabolic pathways had significant positive correlations (r > 0.5, p < 0.01) with dominant fungal species detected in three metagenomes. Taken together, our results indicate that SARS-CoV-2 infection causes significant dysbiosis of fungal microbiome and alters some metabolic pathways and expression of genes in the NT of human. Findings of our study might be helpful for developing microbiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.

“…The non-trivial, timeconsuming and costly nature of microbial analysis (i.e., meta-omics techniques) is arguably a contributing factor to the paucity of microbial characterisation in the field, although the cost and complexity of genetic sequencing has dropped sharply since the early 2000s with the emergence of next-generation sequencing [63]. Nevertheless, the ability to link taxonomic data with functional insights remains limited [64], which is need before a comprehensive picture of metabolic pathways occurring within a given AD system can be drawn. Strengthening public-private partnerships could accelerate knowledge transfer to and put research into practice.…”

Section: Microbial Communitiesmentioning

confidence: 99%

Two Birds with One Stone: Bioplastics and Food Waste Anaerobic Co-Digestion

2022

Following the BBC’s Blue Planet II nature documentary series on marine ecosystems, plastic packaging has come under public fire, with consumers demanding greener alternatives. The biodegradable properties of some bioplastics have offered a potential solution to the global challenge of plastic pollution, while enabling the capture of food waste through anaerobic digestion as a circular and energy-positive waste treatment strategy. However, despite their increasing popularity, currently bioplastics are being tested in environments that do not reflect real-life waste management scenarios. Bioplastics find their most useful, meaningful and environmentally-sound application in food packaging—why is there so little interest in addressing their anaerobic co-digestion with food waste? Here, we provide a set of recommendations to ensure future studies on bioplastic end-of-life are fit for purpose. This perspective makes the link between the environmental sustainability of bioplastics and the role of food waste anaerobic digestion as we move towards an integrated food–energy–water–waste nexus. It shines light on a novel outlook in the field of bioplastic waste management while uncovering the complexity of a successful path forward. Ultimately, this research strives to ensure that the promotion of bioplastics within a circular economy framework is supported across waste collection and treatment stages.