Anthropogenic activities change the relationship between microbial community taxonomic composition and functional attributes

Author(s):  
Lemian Liu ◽  
Shanshan Wang ◽  
Jianfeng Chen
Oryx ◽  
2021 ◽  
pp. 1-9
Author(s):  
Giovany Arturo González-Desales ◽  
Luis Sigler ◽  
Jesús García-Grajales ◽  
Pierre Charruau ◽  
Martha Mariela Zarco-González ◽  
...  

Abstract Negative interactions between people and crocodilians have increased worldwide, but in Mexico there have been few systematic reports and no rigorous evaluation of this problem. We compiled information on negative interactions between people and the spectacled caiman Caiman crocodilus and American crocodile Crocodylus acutus from the Worldwide Crocodilian Attack Database for 1993–2018, and we investigated interactions in greater depth, through interviews with people in La Encrucijada Biosphere Reserve. We examined the relationship between the occurrence of negative interactions between people and C. acutus and the species' nesting season and abundance, and presence records. In Mexico, the frequency of negative interactions increases when anthropogenic activities occur close to nesting sites (< 30 km) and during the nesting season (February–September). In La Encrucijada, following negative interactions with crocodiles, the local inhabitants killed 30 crocodiles measuring > 2.5 m long in 2011–2012. The frequency of negative human–crocodilian interactions was not correlated with the abundance of crocodilians but was correlated with the number of presence records of crocodiles. Strategies to minimize these interactions include warnings at nesting sites, increased monitoring of anthropogenic activities during the nesting season, and management of nests to prevent them being destroyed by people.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
María-Eugenia DeCastro ◽  
Michael P. Doane ◽  
Elizabeth Ann Dinsdale ◽  
Esther Rodríguez-Belmonte ◽  
María-Isabel González-Siso

AbstractIn the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquificae were the two prevalent phyla. An association between the two most prevalent genera, Thermus and Hydrogenobacter, was suggested by the relationship of their metabolism. The high relative abundance of sequences involved in the Calvin–Benson cycle and the reductive TCA cycle unveils the dominance of an autotrophic population. Important pathways from the nitrogen and sulfur cycle are potentially taking place in As Burgas hot spring. In the assembled reads, two complete ORFs matching GH2 beta-galactosidases were found. To assess their functional characterization, the two ORFs were cloned and overexpressed in E. coli. The pTsbg enzyme had activity towards o-Nitrophenyl-β-d-galactopyranoside (ONPG) and p-Nitrophenyl-β-d-fucopyranoside, with high thermal stability and showing maximal activity at 85 °C and pH 6, nevertheless the enzyme failed to hydrolyze lactose. The other enzyme, Tsbg, was unable to hydrolyze even ONPG or lactose. This finding highlights the challenge of finding novel active enzymes based only on their sequence.


Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Denise P. Silva ◽  
Helena D. M. Villela ◽  
Henrique F. Santos ◽  
Gustavo A. S. Duarte ◽  
José Roberto Ribeiro ◽  
...  

Abstract Background Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities. Results The selected multi-domain microbial consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome. Conclusions Our results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and their associated microbiome than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs.


2020 ◽  
Vol 10 (2) ◽  
pp. 116-125
Author(s):  
Georgina Johnson ◽  
Wen San Hii ◽  
Samuel Lihan ◽  
Meng Guan Tay

The presence of microplastics in aquatic systems is mainly due to the anthropogenic activities such as domestic waste dumping. Undeniably, rivers either in urban or suburban areas are always a waste dumpling sites from the surrounding residences. Thus, the purpose of this study was to determine the relationship between microplastic abundance and different degree of urbanization across Kuching in Sarawak. Three sampling locations with different degrees of urbanisation had been studied across Kuching. A total of 137 pieces of microplastics were collected along the study and analysed using stereoscopic microscope for the shape identification and FTIR spectrophotometer for functional groups present in the microplastics. Filament was the most abundant microplastics shape found, whereas the IR results showed that ethylenevinylacetate (9%), polyamides or nylon (15%), polypropylene (42%), poly(methylmethacrylate) (16%) and polystyrene (18%) were found in the study. The most abundant microplastics in the water samples was polypropylene (42%), whereas ethylenevinylacetate (9%) was the least. The degree of urbanisation does not directly relate to the microplastic present in the river system in Kuching City, but the anthropogenic activity is the main factor that affecting the microplastic abundance in the river.   Keywords: anthropologenic activity, FTIR, microplastics, polymer identification, urban, sub-urban


2019 ◽  
Author(s):  
Hsin-Nan Lin ◽  
Yaw-Ling Lin ◽  
Wen-Lian Hsu

ABSTRACTCharacterizing the taxonomic diversity of a microbial community is very important to understand the roles of microorganisms. Next generation sequencing (NGS) provides great potential for investigation of a microbial community and leads to Metagenomic studies. NGS generates DNA fragment sequences directly from microorganism samples, and it requires analysis tools to identify microbial species (or taxonomic composition) and estimate their relative abundance in the studied community. However, only a few tools could achieve strain-level identification and most tools estimate the microbial abundances simply according to the read counts. An evaluation study on metagenomic analysis tools concludes that the predicted abundance differed significantly from the true abundance. In this study, we present StrainPro, a novel metagenomic analysis tool which is highly accurate both at characterizing microorganisms at strain-level and estimating their relative abundances. A unique feature of StrainPro is it identifies representative sequence segments from reference genomes. We generate three simulated datasets using known strain sequences and another three simulated datasets using unknown strain sequences. We compare the performance of StrainPro with seven existing tools. The results show that StrainPro not only identifies metagenomes with high precision and recall, but it is also highly robust even when the metagenomes are not included in the reference database. Moreover, StrainPro estimates the relative abundance with high accuracy. We demonstrate that there is a strong positive linear relationship between observed and predicted abundances.


2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Minghui Liu ◽  
Xin Sui ◽  
Yanbo Hu ◽  
Fujuan Feng

Abstract Background The broad-leaved Korean pine mixed forest is an important and typical component of a global temperate forest. Soil microbes are the main driver of biogeochemical cycling in this forest ecosystem and have complex interactions with carbon (C) and nitrogen (N) components in the soil. Results We investigated the vertical soil microbial community structure in a primary Korean pine-broadleaved mixed forest in Changbai Mountain (from 699 to 1177 m) and analyzed the relationship between the microbial community and both C and N components in the soil. The results showed that the total phospholipid fatty acid (PLFA) of soil microbes and Gram-negative bacteria (G-), Gram-positive bacteria (G+), fungi (F), arbuscular mycorrhizal fungi (AMF), and Actinomycetes varied significantly (p < 0.05) at different sites (elevations). The ratio of fungal PLFAs to bacterial PLFAs (F/B) was higher at site H1, and H2. The relationship between microbial community composition and geographic distance did not show a distance-decay pattern. The coefficients of variation for bacteria were maximum among different sites (elevations). Total soil organic carbon (TOC), total nitrogen (TN), soil water content (W), and the ratio of breast-height basal area of coniferous trees to that of broad-leaved tree species (RBA) were the main contributors to the variation observed in each subgroup of microbial PLFAs. The structure equation model showed that TOC had a significant direct effect on bacterial biomass and an indirect effect upon bacterial and fungal biomass via soil readily oxidized organic carbon (ROC). No significant relationship was observed between soil N fraction and the biomass of fungi and bacteria. Conclusion The total PLFAs (tPLFA) and PLFAs of soil microbes, including G-, G+, F, AMF, and Actinomycetes, were significantly affected by elevation. Bacteria were more sensitive to changes in elevation than other microbes. Environmental heterogeneity was the main factor affecting the geographical distribution pattern of microbial community structure. TOC, TN, W and RBA were the main driving factors for the change in soil microbial biomass. C fraction was the main factor affecting the biomass of fungi and bacteria and ROC was one of the main sources of the microbial-derived C pool.


2015 ◽  
Vol 16 (2) ◽  
pp. 716-725 ◽  
Author(s):  
Xu Zhang ◽  
Qing Gu ◽  
Xi-En Long ◽  
Zhao-Lei Li ◽  
Dong-Xiu Liu ◽  
...  

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