Using Ipomoea aquatic as an environmental-friendly alternative to Elodea nuttallii for the aquaculture of Chinese mitten crab

Elodea nuttallii is widely used in Chinese mitten crab (CMC) rearing practice, but it is not a native aquatic plant and cannot endure high temperature. Thus, large E. nuttallii mortality and water deterioration events could occur during high-temperature seasons. The aim of this study was to identify the use of local macrophytes in CMC rearing practice, including Ipomoea aquatic and Oryza sativa. A completely randomized field experiment was conducted to investigate the crab yield, water quality, bacterioplankton community and functions in the three different systems (E. nuttallii, I. aquatic, and O. sativa). Average crab yields in the different macrophyte systems did not differ significantly. The I. aquatic and O. sativa systems significantly decreased the total nitrogen and nitrate-N quantities in the outflow waters during the rearing period compared to the E. nuttallii system, and the I. aquatic and O. sativa plants assimilated more nitrogen than the E. nuttallii plant. Moreover, the significant changes of bacterioplankton abundances and biodiversity in the three systems implied that cleanliness of rearing waters was concomitantly attributed to the differential microbial community and functions. In addition, principle component analysis successfully differentiated the bacterioplankton communities of the three macrophytes systems. Environmental factor fitting and the co-occurrence network analyses indicated that pH was the driver of bacterioplankton community structure. Functional predictions using PICRUSt (v.1.1.3) software based on evolutionary modeling indicated a higher potential for microbial denitrification in the I. aquatic and O. sativa systems. Notably, the O. sativa plants stopped growing in the middle of the rearing period. Thus, the I. aquatic system rather than the O. sativa system could be a feasible and environmental-friendly alternative to the E. nuttallii system in CMC rearing practice

Actinobacterial Community Structure in Soils Receiving Long-Term Organic and Inorganic Amendments▿ †

The impact of long-term organic and inorganic amendments on the actinobacterial community in soils was studied. Denaturing gradient gel electrophoresis patterns based on the V3 region of 16S rRNA suggested that there was no significant difference between the communities occurring in the different amendments. However, analysis of the clone libraries of the actinobacterial communities by the use of multiple statistical approaches showed that these communities were significantly different from each other. Results showed that long-term organic and inorganic soil amendments did not significantly alter the overall phylogenetic diversity of the actinobacterial communities but did significantly change the community structure

Use of a Green Fluorescent Protein-Based Reporter Fusion for Detection of Nitric Oxide Produced by Denitrifiers

To determine if green fluorescent protein could be used as a reporter for detecting nitric oxide production, gfp was fused to nnrS from Rhodobacter sphaeroides 2.4.3. nnrS was chosen because its expression requires nitric oxide. The presence of the fusion in R. sphaeroides 2.4.3 resulted in a significant increase in fluorescent intensity of the cells, but only when nitrite reductase was active. Cells lacking nitrite reductase activity and consequently the ability to generate nitric oxide were only weakly fluorescent when grown under denitrification-inducing conditions. One of the R. sphaeroides strains unable to generate nitric oxide endogenously was used as a reporter to detect exogenously produced nitric oxide. Incubation of this strain with sodium nitroprusside, a nitric oxide generator, significantly increased its fluorescence intensity. Mixing of known denitrifiers with the reporter strain also led to significant increases in fluorescence intensity, although the level varied depending on the denitrifier used. The reporter was tested on unknown isolates capable of growing anaerobically in the presence of nitrate, and one of these was able to induce expression of the fusion. Analysis of the 16S rRNA gene sequence of this isolate placed it within the Thauera aromatica subgroup, which is known to contain denitrifiers. These experiments demonstrate that this green fluorescent protein-based assay provides a useful method for assessing the ability of bacteria to produce nitric oxide

Lysinimonas yzui sp. nov., isolated from cattail root soil from mine tailings

Mei, Lijuan, Piao, Zhe, Hu, Jian, Shi, Linlin, Bai, Yanchao, Yin, Shixue (2020): Lysinimonas yzui sp. nov., isolated from cattail root soil from mine tailings. International Journal of Systematic and Evolutionary Microbiology 70 (3): 2003-2007, DOI: 10.1099/ijsem.0.00401

Toward tuberculosis elimination by understanding epidemiologic characteristics and risk factors in Hainan Province, China

Abstract Background The disease burden of tuberculosis (TB) was heavy in Hainan Province, China, and the information on transmission patterns was limited with few studies. This atudy aims to further explore the epidemiological characteristics and influencing factors of TB in Hainan Province, and thereby contribute valuable scientific evidences for TB elimination in Hainan Province. Methods The TB notification data in Hainan Province from 2013 to 2022 were collected from the Chinese National Disease Control Information System Tuberculosis Surveillance System, along with socio-economic data. The spatial–temporal and population distributions were analyzed, and spatial autocorrelation analysis was conducted to explore TB notification rate clustering. In addition, the epidemiological characteristics of the cases among in-country migrants were described, and the delay pattern in seeking medical care was investigated. Finally, a geographically and temporally weighted regression (GTWR) model was adopted to analyze the relationship between TB notification rate and socio-economic indicators. The tailored control suggestions in different regions for TB elimination was provided by understanding epidemiological characteristics and risk factors obtained by GTWR. Results From 2013 to 2022, 64,042 cases of TB were notified in Hainan Province. The estimated annual percentage change of TB notification rate in Hainan Province from 2013 to 2020 was − 6.88% [95% confidence interval (CI): − 5.30%, − 3.69%], with higher rates in central and southern regions. The majority of patients were males (76.33%) and farmers (67.80%). Cases among in-country migrants primarily originated from Sichuan (369 cases), Heilongjiang (267 cases), Hunan (236 cases), Guangdong (174 cases), and Guangxi (139 cases), accounting for 53%. The majority (98.83%) of TB cases were notified through passive case finding approaches, with delay in seeking care. The GTWR analysis showed that gross domestic product per capita, the number of medical institutions and health personnel per 10,000 people were main factors affecting the high TB notification rates in some regions in Hainan Province. Different regional tailored measures such as more TB specialized hospitals were proposed based on the characteristics of each region. Conclusions The notification rate of TB in Hainan Province has been declining overall but still remained high in central and southern regions. Particular attention should be paid to the prevalence of TB among males, farmers, and out-of-province migrant populations. The notification rate was also influenced by economic development and medical conditions, indicating the need of more TB specialized hospitals, active surveillance and other tailored prevention and control measures to promote the progress of TB elimination in Hainan Province

Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil

High-throughput sequencing technologies have recently made it possible to interrogate the phylogenetic diversity of soils at considerable depth. This ability has led to the development of many computational tools to infer interaction networks from environmental samples. Although such tools have widely been used, they have more often served as a visual means to compare microbial communities across environmental gradients than as a means to appreciate microbial interactions associated with certain ecological processes. Previous studies have often regarded a subnetwork (module) as a functional unit but its functionality in ecological context has never been evidenced. To make better use of these tools in appreciating microbial interactions, we propose the combinational use of different inference tools. This ensemble approach permits the use of more independent predictors and the removal of tool-specific predictions in order to increase prediction accuracy. The purpose of the present study is to identify ecologically meaningful bacterial associations using multi-tool approach. Soil samples were collected in time series from experimental paddy rice plots. Bacterial communities were characterized by high-throughput tag sequencing of 16S rRNA gene fragments. We used three tools, Co-occurrence Network inference (CoNet), Molecular Ecological Network Analysis (MENA) and extended Local Similarity Analysis (eLSA), to infer networks from abundance profiles, partitioned the networks into modules, screened for the modules with ≥50% of genus-/species-level nodes, captured the modules that were derived from different tools and shared ≥ 50% of order-level nodes (tool-agreed modules) and tested their robustness against the changes in the tool parameters. By these procedures, two three-tool-agreed modules were found. One represented a guild that is phenotypically associated with aerobic respiration and fermentation and the other represented a guild phenotypically associated with metal/sulphur cycles, all of which are essential processes of water-submerged paddy soils that are mediated by bacteria. These data suggested that the linked members in a module were functionally associated taxa that work together to achieve a distinct function or an ecological process, and thus were ecologically meaningful to the environment. We selected three linked species from a three-tool-agreed module and validated their interactions using co-culture methods. Results showed that the interaction type between Janthinobacterium lividum and Leuconostoc lactis in the two-species mixture was validated to be ambivalent, positive for one partner and negative for the other. However, this type of interaction was not retained when a third party Lactococcus piscium was introduced, signifying the complexity of multi-species interactions. Validation results suggested that the selected species were interacting partners in laboratory but the validated interaction types were different from those inferred. By multi-tool approach, we also found that highly linked nodes, which are often referred to as “keystone species” and are frequently interpreted as the species playing important roles in soils, are tool dependent. Among top ten highly linked nodes, only four are conserved across three tools. These results suggest more research is required on the ecological significance of degree-based identification of keystone species. Overall, the present study highlights the potential utility of combined use of inference tools to identify ecologically meaningful bacterial associations in soils and other environmental samples. It is interesting to see what type of ecologically meaningful bacterial associations can be found in other soils.publisher: Elsevier articletitle: Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil journaltitle: Soil Biology and Biochemistry articlelink: http://dx.doi.org/10.1016/j.soilbio.2016.11.029 content_type: article copyright: © 2016 The Authors. Published by Elsevier Ltd.status: publishe

Additional file 1 of Toward tuberculosis elimination by understanding epidemiologic characteristics and risk factors in Hainan Province, China

Additional file 1: Figure S1. EAPC of TB notification rate by age and gender in Hainan Province from 2013 to 2022. Figure S2. Annual trend of TB notification rate in Hainan Province from 2013 to 2022. Figure S3. Monthly notification number and rate of TB in different cities and counties in Hainan Province from 2013 to 2022. Table S1. Moran's I index results of notification rate of TB at the city/county level in Hainan. Table S2. LISA of TB notification rate in Hainan Province. Figure S4. Changes in the notification rate of TB with age in Hainan Province from 2013 to 2022. Table S3. TB cases with different population characteristics in Hainan Province from 2013 to 2022. Figure S5. Time distribution of TB cases from outside Hainan Province. Figure S6. Age and gender distribution of migrant TB cases outside Hainan Province. Figure S7. Occupational distribution of migrant TB cases outside Hainan Province. Figure S8. Notification distribution of TB patients in Hainan Province from 2013 to 2022. Table S4. Patient delay situation of TB patients in Hainan Province. Table S5. Influencing factors for TB in Hainan Province from 2013 to 2022. Table S6. Results from GTWR model analysis. Figure S9. TB notification rate in regions with low TB notification rate last decade and future prediction. Figure S10. TB notification rate in regions with medium TB notification rate last decade and future prediction. Figure S11. TB notification rate in regions with high TB notification rate last decade and future prediction. Table S7. Main risk factors influencing the prevalence of TB in different cities and counties

Ralstonia solanacearum pathogen disrupts bacterial rhizosphere microbiome during an invasion

Plant pathogen invasions are often associated with changes in physical environmental conditions and the composition of host-associated rhizosphere microbiome. It is however unclear how these factors interact and correlate with each other in determining plant disease dynamics in natural field conditions. To study this, we temporally sampled the rhizosphere of tomato plants that were exposed to moderate to aggressive Ralstonia solanacearum pathogen invasions over one crop season. We found that physiochemical soil properties correlated weakly with the severity of pathogen invasion apart from the water-soluble nitrogen concentration, which increased more clearly during the aggressive invasion. Instead, a much stronger link was found between pathogen invasion and reduced abundance and diversity of various rhizosphere bacterial taxa, simplification of bacterial interaction networks and loss of several predicted functional genes. We further verified our results in a separate greenhouse experiment to show that pathogen invasion causally drives similar changes in rhizosphere microbiome diversity and composition under controlled environmental conditions. Our results suggest that R. solanacearum invasion disrupts rhizosphere bacterial communities leading to clear reduction in the diversity and abundance of non-pathogenic bacteria. These changes could potentially affect the likelihood of secondary pathogen invasions during following crop seasons as less diverse microbial communities are also often less resistant to invasions. Strong negative correlation between pathogen and non-pathogenic bacterial densities further suggest that relative pathogen abundance could better predict the severity of bacterial wilt disease outbreaks compared to absolute pathogen abundance. Monitoring the dynamics of whole microbiomes could thus open new avenues for more accurate disease diagnostics in the future