Stability Of Microbial Community Structure Research Articles

Effects of inoculation with a binary mixture of Lactobacillus plantarum and Leuconostoc citreum on cell wall components of Chinese Dongbei suancai

This study aimed to investigate the effects of inoculation with a starter culture consisting of Lactobacillus plantarum LNJ002 and Leuconostoc citreum BNCC 194779 on microbial community, cell wall polysaccharide characteristics, cell wall degrading enzymes, and microstructure during Chinese Dongbei suancai fermentation. The results showed that Lactobacillus (98.75%) was the dominant genus during fermentation of Dongbei suancai. The principal coordinates analysis (PCoA) suggested that inoculation with Lactobacillus promoted the stability of microbial community structure during Chinese Dongbei suancai fermentation. Besides, the lower content in cellulose (80.28 ± 2.61 ug/mg) and pectin (53.56 ± 2.67 ug/mg) observed in the inoculated fermented suancai. Simultaneously, the inoculated fermented suancai had the most decreases in SR 1 (70.35%) and SR 3 (72.06%) and the most increase in SR 2 (950%), which suggested that inoculation intensified the decrease of the linearity and the RG-1 branching degree of pectin. The contents of polygalacturonase (PG) and pectin methylesterase (PME) in inoculated fermented suancai were 21.06% and 21.86% higher than those in naturally fermented suancai. In addition, the surface of suancai leaves gradually changed from smooth to rough during fermentation, which was accelerated by inoculation. Moreover, Lactobacillus, Aspergillus, Wallemia and Mucor were all negatively correlated with cellulose and GalA. These results revealed that inoculation promoted the formation of dominant genus structure during suancai fermentation, changed the effects of enzymes on the degradation of cell wall components, thereby accelerated the formation of Chinese Dongbei suancai texture.

[Spatial-temporal Changes and Driving Factors of Soil Microbial Communities in a Typical City of North China Plain].

The structure and function of microbial communities are affected by several environmental factors. To clarify the spatial-temporal changes and main influencing factors of soil microbial communities in a typical pharmaceutical city, it is urgent to study the spatial-temporal changes in microbial communities in soils for typical cities. Shijiazhuang City was selected as the study area, and 12 sampling sites were selected. The topsoil was collected in June (summer) and September (autumn) of 2021. The 16S rRNA high-throughput sequencing technology was used to study the structure and function of microbial communities in the soil and explore their spatial-temporal changes. Concurrently, Pearson correlation analysis was applied to establish the correlation between the microbial community and environmental factors, and identify the main driving factors of temporal and spatial changes in the microbial community. The results showed that:① Actinobaciota and Proteobateria were the main dominant bacteria in the surface soil of Shijiazhuang City; at the phylum level, the relative abundance of Actinobacteria and Proteobateria decreased from summer to autumn; at the genus level, the dominant genera were Arthrobacter and unknown genera in summer and Arthrobacter and Candidatus_Nitrocosmicus in autumn, which showed significant seasonal differences (P<0.05). ② For seasonal variation, the mean values of the Simpson, Ace, and Chao indices increased, whereas the mean values of OTU decreased; for spatial variation, the Shannon and Simpson indices showed significant spatial difference (P<0.01 and P<0.05). ③ There were no significant spatial-temporal differences in various functional genes; thereinto, the relative abundances of energy production and transformation functional genes were the highest (24.06%-24.84% in summer and 24.63%-25.98% in autumn, respectively). ④ The compositions of microbial community, diversity index, and functional genes were significantly correlated with quinolone antibiotics (QNs), total phosphorus (TP), and nitrate nitrogen (NO3--N), most significantly correlated with QNs (|r|>0.900), which indicated that antibiotics were the main driving factor of soil microbial communities. Therefore, to ensure the stability of microbial community structure and function in urban soil, the comprehensive management and control of antibiotic pollution in soil should be further strengthened.

Stable partial nitritation of mature landfill leachate in a continuous flow bioreactor: Long-term performance, microbial community evolution, and mechanisms

A continuous flow bioreactor was operated for 300 days to investigate partial nitritation (PN) of mature landfill leachate, establishing the long-term performance of the system in terms of the microbial community composition, evolution, and interactions. The stable operation phase (31–300 d) began after a 30 days of start-up period, reaching an average nitrite accumulation ratio (NAR) of 94.43% and a ratio of nitrite nitrogen to ammonia nitrogen (NO2−-N/NH4+-N) of 1.16. Some fulvic-like and humic-like compounds and proteins were effectively degraded in anaerobic and anoxic tanks, which was consistent with the corresponding abundance of methanogens and syntrophic bacteria in the anaerobic tank, and organic matter degrading bacteria in the anoxic tank. The ammonia-oxidizing bacteria (AOB) Nitrosomonas was found to be the key functional bacteria, exhibiting an increase in abundance from 0.27% to 6.38%, due to its collaborative interactions with organic matter degrading bacteria. In-situ inhibition of nitrite-oxidizing bacteria (NOB) was achieved using a combination of free ammonia (FA) and free nitrous acid (FNA), low dissolved oxygen (DO) with fewer bioavailable organics conditions were employed to maintain stable PN and a specific ratio of NO2−-N/NH4+-N, without an adverse impact on AOB. The synergistic relationships between AOB and both denitrifying bacteria and organic matter degrading bacteria, were found to contribute to the enhanced PN performance and microbial community structure stability. These findings provide a theoretical guidance for the effective application of PN-Anammox for mature landfill leachate treatment.

Effects of light intensity and photoperiod on the cultivation of the soft coral Sarcophyton trocheliophorum

Coral reefs are one of the most diverse, productive ecosystems in the world, and light plays crucial role in its survival. Notably, the effects of light conditions on soft coral and its adaptive mechanism were unclear. Thus, the present study aimed to investigate and evaluate the effects of different light intensities (30, 80 and 130 μmol m−2 s−1) and photoperiods (18D:6L, 12D:12L and 6D:18L) on cultivation of soft coral Sarcophyton trocheliophorum. During two 50-day of the experiments, we monitored the zooxanthellae density, Chl a content, enzyme activities (SOD, CAT and GST) and microbial diversity of S. trocheliophorum. Our study's outcomes found that, at the end of the experiment, the 80 μmol m−2 s−1 light intensity group and 12D:12L photoperiod group both possessed the highest zooxanthellae density (2.54 × 108 ± 0.14 × 108 cells g−1 DW and 2.40 × 108 ± 0.07 × 108 cells g−1 DW, respectively), Chl a content (295.01 ± 14.13 μg g−1 DW and 287.78 ± 16.13 μg g−1 DW, respectively) and microbial diversity and relatively stable enzyme activities level. Besides, we speculated that the reason for the decline of zooxanthellae density, Chl a content and microbial diversity under other light conditions might be that it induced light stress and caused oxidative damage. The main bacterial composition of S. trocheliophorum in different light conditions was similar at the phylum level, showing the stability of microbial community structure. Proteobacteria, Actinobacteria and Firmicutes were dominant under all light conditions, so we hypothesized that these bacteria phylum play a crucial role in coral growth and survival.In conclusion, compared with the other treatments, 80 μmol m−2 s−1 light intensity and 12D:12L photoperiod were more beneficial to the growth performance of S. trocheliophorum and could be recommended for its cultivation condition. Our study could provide helpful information for sustainable management plans for the cultivation and conservation of soft corals, which was especially important to the protection and restoration of degraded coral reefs.

Ecological niche differences regulate the assembly of bacterial community in endophytic and rhizosphere of Eucalyptus

The relationship between microorganisms and plants has been a hot topic of research because of its direct link to plant health and productivity, and these interactions are not limited to the soil. The structural and ecological variation of bacterial communities due to spatial isolation in different parts of plants is still unclear. Whether intensive management of Eucalyptus plantations affects this variation should also be concerned. To investigate the mechanisms underlying bacterial changes in different ecological niches of Eucalyptus and the stability of bacterial communities after continuous high-intensity planting of Eucalyptus, we studied the effects of long-term plantation of Eucalyptus on the structure, assembly patterns, and interactions of the bacterial community. Woodlands that planted with Eucalyptus urophylla S.T. Blake × Eucalyptus grandis Hill ex Maiden (Eucalyptus urograndis, hereafter E. urograndis) in three generations (10 years after planting) were selected for study, and the woodlands were cleared and replanted with E. urograndis. Rhizosphere soil, roots, stems, branches, and leaves of E. urograndis differing in age (2, 4, and 6 years) after planting were sampled, and the rhizosphere soil bacteria and endophytic bacterial communities of different parts were determined using the 16S rRNA technique. We detected structural variation in the soil and endophytic bacterial communities as well as variation in community assembly. Stochastic processes made large contributions to the assembly of highly abundant soil bacterial communities, as well as low-abundant endophytic bacterial communities of the branches and leaves (especially leaves), and this pattern may be strongly related to the ecological niches of the bacteria. The bacterial correlation network demonstrated that the properties of Eucalyptus soil and their endophytic bacterial communities can vary 6 years after successive plantings. Thus, measures should be taken to ecologically restore Eucalyptus woodlands after 15 years of high-intensity planting to ensure the stability of microbial community structure, the maintenance of adequate ecological properties during Eucalyptus planting, and the sustainable production and management of Eucalyptus plantations.

Responses of two marine fish to organically complexed Zn: Insights from microbial community and liver transcriptomics

The diversity and adjustability of metal-organic complex enhance the function of metals and promote the burgeoning fields of chemical biology. In the present study, we chose two marine fish to explore the effects of a dihydromyricetin (DMY)-Zn(II) complex on the intestinal microbiome composition and liver biological function using high-throughput sequencing technology. Two economic fish species commonly found in Southern China (golden pompano Trachinotus ovatus and pearl gentian grouper ♀Epinephelus fuscoguttatus × ♂Epinephelus lanceolatus) were exposed to dietary DMY-Zn complex for 4-week. Our study found that DMY-Zn performed a vital function on the improved anti-oxidative ability of both fish species. The Zn complex improved the stability of microbial community structure of the golden pompano by enhancing the α-diversity, but its impacts on the composition and diversity of intestine microorganisms of grouper were insignificant. BugBase results showed that the intestine microbiota following DMY-Zn exposure contained a lower abundance of potentially pathogenic bacteria and higher abundance of aerobic bacteria. Intestine health and utilization of carbohydrates were improved in the golden pompano, and unclassified bacteria were significantly enriched in the grouper. Liver transcriptome indicated that DMY-Zn affected the oxidative phosphorylation process (OXPHOS). Specifically, the OXPHOS process (map00190) was activated by promoting the glucose uptake (map04251, map04010) in golden pompano and lipid metabolism (map00071, map00140, map00062 and map00564) in grouper. Such difference in the responses of intestine microbiome and liver metabolism may be possibly explained by their different Zn basal requirements. Our study demonstrated that different fish species may have different responses to dietary DMY-Zn complex. The results provided a reference for the application of new additives in aquatic animal feed, and new insights into the roles of metal-organic complex in their biological impacts on fish.

Decomposition of different crop straws and variation in straw-associated microbial communities in a peach orchard, China

Crop residue is a major source of soil organic matter; therefore, application of crop straw to soil contributes to the sustainable development of organic agriculture. To better understand the transformation of crop straw in orchard soils, we investigated the relationship between the characteristics of straw decomposition and functional diversity of associated microbial communities in a long-term peach orchard, China. Mesh bags, each containing 30 g of corn or bean straw, were buried at a soil depth of 20 cm in a 12-year-old peach orchard for 360 d (October 2011–October 2012). Three treatments were applied, i.e., fresh corn straw, fresh corn straw with nitrogen fertilizer (urea, 10.34 g/kg), and fresh bean straw. Changes in straw residual rate, straw water content and soil conditions were monitored after treatment. The functional diversity of straw-associated microbial communities was analyzed by the Biolog-Eco microplate assay. During the decomposition process, straw residual rates did not vary considerably from 10 d (30.4%–45.4%) to 360 d (19.0%–30.3%). Irrespective of nitrogen addition, corn straw decomposed faster than bean straw. Corn straw with nitrogen fertilizer yielded the highest average well color development (AWCD) values (1.11–1.67), followed by corn straw (1.14–1.68) and bean straw (1.18–1.62). Although the AWCD values did not differ significantly among the three treatments, substantial differences occurred across various time periods of the decomposition process (P<0.01). In terms of carbon source utilization, the dominant microbial groups fed mainly on saccharides. Hard-to-decompose substances gradually accumulated in the middle and late stages of straw decomposition. Of the six categories of carbon sources tested, the utilization rate of aromatics was the lowest with corn straw, whereas that of polymers was the lowest with bean straw. Among different treatments, straw residual rate was negatively correlated to soil available phosphorous, soil available potassium and soil temperature (P<0.05), but not to soil water content. In some cases (corn straw with or without nitrogen fertilizer), straw residual rate was negatively correlated to straw water content, amino acid utilization and carboxylic acid utilization, and positively correlated with microbial species richness and evenness (P<0.05). Microbial community associated with corn and bean straw decomposition in soil was respectively dominated by aromatic- and polymer-metabolizing groups during the middle and late stages of this process, which could reduce the stability of microbial community structure and decrease the rate of straw decomposition in fruit tree orchard.

A Review on Airborne Microbes: The Characteristics of Sources, Pathogenicity and Geography

Microbes are widespread and have been much more studied in recent years. In this review, we describe detailed information on airborne microbes that commonly originate from soil and water through liquid–air and soil–air interface. The common bacteria and fungi in the atmosphere are the phyla of Firmicutes, Proteobacteria, Bacteroides, Actinobacteria, Cyanobacteria and Ascomycota, Basidiomycota, Chytridiomycota, Rozellomycota that include most pathogens leading to several health problems. In addition, the stability of microbial community structure in bioaerosols could be affected by many factors and some special weather conditions like dust events even can transport foreign pathogens to other regions, affecting human health. Such environments are common for a particular place and affect the nature and interaction of airborne microbes with them. For instance, meteorological factors, haze and foggy days greatly influence the concentration and abundance of airborne microbes. However, as microorganisms in the atmosphere are attached on particulate matters (PM), the high concentration of chemical pollutants in PM tends to restrain the growth of microbes, especially gathering atmospheric pollutants in heavy haze days. Moreover, moderate haze concentration and/or common chemical components could provide suitable microenvironments and nutrition for airborne microorganism survival. In summary, the study reviews much information and characteristics of airborne microbes for further study.

Magnetic field enhanced denitrification efficiency of immobilized bacterial particles

The effect of the magnetic field on denitrification process in immobilized bacteria particles was investigated in this study. The magnetic field could enhance the denitrification efficiency, especially for wastewater with low C/N ratios, and the average removal efficiencies of NO3 --N increased by 6.58%. High-throughput sequencing analysis revealed that the magnetic field had substantial impacts on the stability of microbial community structure and relative abundance in immobilized bacteria particles, which was beneficial for the stability of denitrifying bacteria. Through the research in this paper, we suggest that magnetic field can be used to improve the denitrification performance of immobilized bacteria particles in the wastewater treatment industry.

New insights into the metagenomic link between pre‐treatment method, addition of an inoculum and biomethane yield during anaerobic digestion of water hyacinth (Eichhornia crassipes)

AbstractBACKGROUNDWater hyacinth (Eichhornia crassipes) is a fast growing water weed that threatens the aquatic ecosystem and human activities, hence control of the plant is essential. One such control approach is to harvest and utilize hyacinth as a substrate for anaerobic digestion (AD). Various factors influence AD performance, including substrate pre‐treatment and microbial community composition, amongst others. This study was aimed at establishing the link between method of substrate pre‐treatment, microbial diversity, inoculum addition and biogas yield during AD of hyacinth.RESULTSThe addition of an inoculum resulted in microbial community stability and early biomethane production of up to 0.4 L irrespective of pre‐treatment method. However, cultures that lacked inoculum showed distinct microbial community structure variation in response to pre‐treatment method, and minimal early biomethane production (up to 0.1 L). Biogas produced by cultures lacking inoculum was initially mostly composed of carbon dioxide (up to 100% of total biogas), but as digestion proceeded, an increase in biomethane production was observed (up to 60% of total biogas), which correlated with the shift in microbial community structure and increased microbial diversity. This indicates the presence of biogas‐producing microorganisms associated with the collected hyacinth. Canonical correspondence analysis proved that dynamic changes in microbial community structure and biogas yield were strongly correlative.CONCLUSIONThis study proves that hyacinth pre‐treatment influences microbial community structure and concomitant biogas yield in the absence of an inoculum. The addition of an inoculum aids in stability of microbial community structure and biogas yield irrespective of method of hyacinth pre‐treatment. © 2019 Society of Chemical Industry

Agricultural management affects the response of soil bacterial community structure and respiration to water-stress

Soil microorganisms are responsible for organic matter decomposition processes that regulate soil carbon storage and mineralisation to CO2. Climate change is predicted to increase the frequency of drought events, with uncertain consequences for soil microbial communities. In this study we tested the hypothesis that agricultural management used to enhance soil carbon stocks would increase the stability of microbial community structure and activity in response to water-stress. Soil was sampled from a long-term field trial with three soil carbon management systems and was used in a laboratory study of the effect of a dry–wet cycle on organic C mineralisation and microbial community structure. After a drying–rewetting event, soil microcosms were maintained wet and microbial community structure and abundance as well as microbial respiration were measured for four weeks. The results showed that the NO-TILL management system, with the highest soil organic matter content and respiration rate, had a distinct bacterial community structure relative to the conventional and the TILL without fertiliser systems. In all management systems, the rewetting event clearly modified microbial community structure and activity. Both returned to their pre-drought state after 28 days. However, the magnitude of variation of C mineralisation was lower (i.e. the resistance to stress was higher) in the NO-TILL system. The genetic structure of the NO-TILL bacterial communities was most modified by water-stress and exhibited a slower recovery rate. This suggests that land use management can increase microbial functional resistance to drought stress via the establishment of bacterial communities with particular metabolic capacities. Nevertheless, the resilience rates of C mineralisation were similar among management regimes, suggesting that similar mechanisms occur, maybe due to a common soil microbial community legacy.

Microbial community structure stability, a key parameter in monitoring the development of constructed wetland mesocosms during start-up

Constructed wetlands (CWs) are known to be effective for treating waste streams, and pilot-scale CWs are useful for assessing the impact of pollutants and their remediation. However, little is known with respect to the establishment of these mesocosm systems or the parameters which should be monitored in assessing system equilibration, i.e. when they present stabilised physical and biological patterns. The aim of this study was to evaluate the temporal aspects of CW equilibration as a basis for future studies of system response to amendment. Microbial biomass and hydraulic conductivity values were monitored and microbial community fingerprints were obtained using denaturing gradient gel electrophoresis (DGGE). This study showed that microbial community fingerprinting provides a valuable tool for assessing the time scales of equilibration, as it was the last parameter which stabilised during the equilibration period. Hydraulic conductivity was also an important parameter in determining the time scale for initiation of the equilibration process during the study. For a CW of the dimensions used (173 cm long/106 cm large/30 cm depth), community equilibration times demonstrated on the basis of similar microbial community structures were found to be on the order of 100 days.

Correlation of Community Dynamics and Process Parameters As a Tool for the Prediction of the Stability of Wastewater Treatment

Wastewater treatment often suffers from instabilities and the failure of specific functions such as biological phosphorus removal by polyphosphate accumulating organisms. Since most of the microorganisms involved in water clarification are unknown it is challenging to operate the process accounting for the permanent varying abiotic parameters and the complex composition and unrevealed metabolic capacity of a wastewater microbial community. Fulfilling the demands for water quality irrespective of substrate inflow conditions may emit severe problems if the limited management resources of municipal wastewater treatment plants are regarded. We used flow cytometric analyses of cellular DNA and polyphosphate to create patterns mirroring dynamics in community structure. These patterns were resolved in up to 15 subclusters, the presence and abundances of which correlated with abiotic data. The study used biostatistics to determine the kind and strength of the correlation. Samples investigated were obtained from a primary clarifier and two activated sludge basins. The stability of microbial community structure was found to be high in the basins and low in the primary clarifier. Despite major abiotic changes certain subcommunities were dominantly present (up to 80% stability), whereas others emerged only sporadically (down to 3% stability, both according to equivalence testing). Additionally, subcommunities of diagnostic value were detected showing positive correlation with substrate influxes. For instance blackwater (r(s) = 0.5) and brewery inflow (both r(s) = 0.6) were mirrored by increases in cell abundances in subclusters 1 and 6 as well as 4 and 8, respectively. Phosphate accumulation was obviously positively correlated with nitrate (r(s) = 0.4) and the presence of denitrifying organisms (Rhodacyclaceae). Various other correlations between community structure and abiotic parameters were apparent. The bacterial composition of certain subcommunities was determined by cell sorting and phylogenetic tools like T-RFLP. In essence, we developed a monitoring tool which is quick, cheap and causal in its interpretation. It will make laborious PCR based technique less obligatory as it allows reliable process monitoring and control in wastewater treatment plants.