Metagenomic exploration of bacterial community shifts before, during, and after passage through earthworm Eutyphoeus waltoni.

Shifts in bacterial and archaeal communities, associated with changes in chemical profiles, were investigated in an anaerobic batch reactor treating dairy-processing wastewater prepared with whey permeate powder. The dynamics of bacterial and archaeal populations were monitored by quantitative real-time PCR and showed good agreement with the process data. A rapid increase in bacterial populations and a high rate of substrate fermentation were observed during the initial period. Growth and regrowth of archaeal populations occurred with biphasic production of methane, corresponding to the diauxic consumption of acetate and propionate. Bacterial community structure was examined by denaturing gel gradient electrophoresis (DGGE) targeting 16S rRNA genes. An Aeromonas-like organism was suggested to be mainly responsible for the rapid fermentation of carbohydrate during the initial period. Several band sequences closely related to the Clostridium species, capable of carbohydrate fermentation, lactate or ethanol fermentation, and/or homoacetogenesis, were also detected. Statistical analyses of the DGGE profiles showed that the bacterial community structure, as well as the process performance, varied with the incubation time. Our results demonstrated that the bacterial community shifted, reflecting the performance changes and, particularly, that a significant community shift corresponded to a considerable process event. This suggested that the diagnosis of an anaerobic digestion process could be possible by monitoring bacterial community shifts.

To date, there have been few reports examining the correlation between biochar treatments, crop species, and microbiome shifts. In this study, shifts in the soil bacterial community were investigated 4 years after a single incorporation of biochar in soils planted with soybeans and maize. Clear changes in the bacterial community composition and structure were detected in the soybean-planted soil amended with low-titer biochar (7.89 t/ha), whereas such changes in the maize-planted soil were not observed at the same biochar amendment rate, suggesting a more sensitive influence on the bacterial community in the soybean-planted soil than that in the maize-planted soil. Bacterial abundance in the maize-planted soil was reduced significantly with increasing biochar addition (15.78 and 47.34 t/ha), which was probably due to the inhibitory substances originating from biochar. Both the bacterial community and biomarkers in soil under biochar amendment varied with planted crops, bacterial communities responding differently to biochar amendment. All these results suggested that biochar might influence the bacterial community in maize- and soybean-growing soils under different mechanisms. Our findings should be valuable for an in-depth understanding of the potential mechanism of soil microbiome changes following biochar incorporation and for biochar application in agriculture.

Salinity and drought are the major abiotic stresses that limit agricultural productivity. Application of plant growth promoting rhizobacteria (PGPR) is an attractive technology but with the bottlenecks of reduced efficacy and survivability in the environment. For increased efficiency of PGPR strains, the impact of stresses on the native bacterial community needs to be studied. Experimentally induced stresses would be ideal to assess the immediate perturbances in the structure of soil bacterial community. Hence, the study focused on the effect of experimentally-induced salinity, and drought stress on rhizospheric bacterial community of Cajanus cajan. A plant growth experiment was set up to induce salinity and drought stresses. Shifts in the bacterial community were assessed by a culture-independent technique of denaturing gradient gel electrophoresis using 16S ribosomal RNA gene and transcript as markers, leading to a comparison of the resident with the active bacterial community. The impact on plant was evaluated by measurement of plant biometrics. Further, salinity and drought-stressed conditions led to distinct shifts in native and active rhizospheric bacterial community, corresponding to the higher decline at induction of stresses, and stabilization at later time points. The study encompasses the perturbations in the active and resident rhizospheric bacterial community caused by the induction of two different abiotic stresses along the plant's growth.

The search for disease-associated compositional shifts in bowel bacterial communities of humans

Distinct bacterial community and diversity shifts after phytoplankton-derived dissolved organic matter addition in a coastal environment

Sedimentary records covering the Late Pleistocene show glacial-interglacial and millennial temperature changes accompanied with, for instance, rainfall and vegetation changes at the global and regional scales. However, such records are missing for the islands of Macaronesia. Here we generate three sedimentary records over the last 10,000 to 45,000 years from the islands of Tenerife, Gran Canaria, and La Gomera using glycerol dialkyl glycerol tetraethers (GDGTs). At the global scale, air temperature and soil pH influence GDGT distributions in soils, although these biomarkers also react to other environmental factors (e.g., land use, vegetation, and soil moisture and chemistry) and shifts in bacterial and archaeal communities. Accordingly, we examined several GDGT-based proxies, notably those using bacterial branched GDGTs (brGDGTs), to assess their applicability in the Canary Islands. Our preliminary results show drastic downcore and inter-site changes in GDGT distributions, with brGDGT-based air temperature ranges larger than 10 °C over the last 10,000 to 45,000 years when applying global calibrations at the three study sites. Air temperatures and soil pH inferred from brGDGTs decrease in Tenerife and La Gomera over the end of the African Humid Period, which suggests an effect of reduced rainfall on brGDGTs, possibly accompanied with a shift in bacterial communities. Air temperatures inferred from brGDGTs show a general increase over the last 27,000 years in Gran Canaria, whereas cyclization and isomerization indices of brGDGTs suggest typically opposite changes in soil pH, in disagreement with global-scale patterns from surficial soils. Our GDGT-based records also show a few drastic increases in archaeal GDGT abundances relative to the full GDGT pool after the Last Glacial Maximum, notably in Gran Canaria and La Gomera, partly related to the rainfall increase during the African Humid Period. Our preliminary application of GDGT-based proxies in the Canary Islands reveals complex environmental influences on soil bacterial and archaeal lipids, which may also be related with local climate and vegetation dynamics. Our preliminary study also motivates a follow-up GDGT study in surficial soils from the Canary Islands to establish, for instance, a brGDGT-temperature calibration suitable for this archipelago.

Bacteria present in fresh extended boar semen may impair the fertility of artificial insemination doses in swine. To date, information regarding the presence or composition of bacterial communities within the boar’s urogenital tract is lacking. These unexplored communities may contribute to the bacterial composition of semen and thereby influence boar fertility. Moreover, hormonal and anatomical changes that occur during puberty could also alter the urogenital tract bacterial communities. Therefore, the objective of this study was to evaluate pre- and post-pubertal shifts in bacterial communities and diversity in boar urogenital tissues (i.e., testis, epididymis, seminal vesicle, prostate, bulbourethral gland, bladder, and preputial diverticulum) using 16S rRNA gene amplicon community sequencing. Crossbred boars were euthanized at 74 ± 2 days of age (pre-pubertal; n = 4) or 276 ± 3 days of age (post-pubertal; n = 6), and intact reproductive tracts were harvested. Sterile swab samples were collected from each tissue of interest for microbiota analysis, and plasma was collected to analyze circulating hormone concentrations of testosterone and dihydrotestosterone. Circulating testosterone was greater (P < 0.01) in post-pubertal boars compared to pre-pubertal boars (3.01 ± 0.26 vs. 0.96 ± 0.36 ng/mL) yet no differences were observed in dihydrotestosterone concentrations. The relative abundance of the phylum Firmicutes was elevated (P < 0.05) in the testis, epididymis, seminal vesicle, bulbourethral gland, and preputial diverticulum of pre-pubertal boars and negatively correlated (P < 0.05) with testosterone. Alternatively, the relative abundance of the phylum Proteobacteria was greater in those same tissues from post-pubertal boars (P < 0.05) and was positively correlated (P < 0.05) with testosterone. Alpha-diversity was reduced in the urogenital tracts of post-pubertal boars compared to pre-pubertal boars (P < 0.01). The bladder had greater alpha-diversity compared to other tissues (P < 0.05). Pre- and post-pubertal boar urogenital tissues have distinct bacterial communities and shifts in these communities following puberty attainment may be associated with elevated testosterone. Future research is warranted to compare bacterial compositions of the boar urogenital tissues to the animal’s ejaculate, which would provide greater insight into the origin of bacteria within boar semen.

Shifts in benthic bacterial communities associated with farming stages and a microbiological proxy for assessing sulfidic sediment conditions at fish farms

Molecular assessment of shift in bacterial community in response to Congo red

Efforts to reduce our use of nitrogen fertilizers have been increasing due to their environmental consequences on soil and ecosystem health. Legume non-legume intercropping systems have been proven as a method to reduce our use of nitrogen fertilizers while maintaining yields. The pea-canola (Pisum sativum-Brassica napus) intercropping system (peaola) has shown promise as its highest yields are with minimal to no nitrogen fertilizer application. Therefore, the goal of our study was to determine how nitrogen fertilization impacts the bacterial community and its predicted function in peaola to aid in agricultural sustainability initiatives. To accomplish this goal, we investigated 1) how the bacterial community was altered in composition and predicted function under three different nitrogen fertilizer application rates (0, 33, and 67 kg N ha-1) in the soil and rhizosphere; and 2) how the concentration of nitrogen was impacted in peaola across different fertilizer application rates. Overall, we found that plant species was the primary factor responsible for differences in the diversity, structure, and predicted function of the rhizosphere bacterial community demonstrating the plants ability to control their rhizosphere community composition. In bulk soil, we didn’t observe differences between cropping systems for the bacterial communities, but fertilizer treatment alone did cause shifts in the community diversity. No significant differences were found in the concentrations of nitrate, nitrite, and ammonia in peaola across fertilizer treatments. This suggests that the changes observed within the bacterial community could reflect shifting plant nutritional needs, leading to plants receiving the necessary levels of nitrogen to thrive.

This study aimed to induce a shift in a bacterial community by adding substrate into a biofloc system to characterize this shift and estimate its benefits in improving water quality and aquatic animal growth. We compared the bacterial communities between two biofloc systems, either with (sB treatment) or without (nB treatment) the addition of substrate (elastic solid packing filler), and we also analyzed the effects of the shift on the water quality and growth performance of shrimp (Litopenaeus vannamei). Beta diversity analysis indicated that the bacterial communities in the two treatments were significantly different (Jaccard index 0.94 ± 0.01, pseudo-F = 3.96, p = 0.001). The addition of substrate showed significant positive effects on bacterial alpha diversity indices (Shannon, Heip, Pielou, and Simpson; p &lt; 0.05) and the abundances of beneficial genera (e.g., Arenimonas, Arthrobacter, Exiguobacterium, Leadbetterella, Luteolibacter, Marinobacter, Nitratireductor, Novosphingobium, Thermomonas, Plesiocystis, and Rubrivivax; p &lt; 0.05). In addition, the substrate also showed significant positive effects on water quality parameters (TAN, TSS, turbidity, biofloc volume, pH, and carbonate alkalinity; p &lt; 0.05), and it also significantly improved shrimp zootechnical performance indices (survival rate, feed conversion ratio, and productivity; p &lt; 0.05). Redundancy analysis revealed that 94.25–98.58% of the variation in the water quality and the shrimp growth performance between the two treatments could be attributed to the shift in bacterial composition and diversity induced by the addition of substrate. These findings characterize the shift in the microbial community in the biofloc system induced by the substrate, and demonstrate how this shift could be beneficial to the water quality and the growth performance of shrimp.

Dynamics of soil resistome and bacterial composition following multi-year application of different antibiotic fermentation residues

Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1) How do water quality and bacterial community composition change along a coastal shelf gradient? (2) Which water quality parameters influence bacterial community composition? (3) Is there a difference in bacterial community composition among the investigated habitats? For this purpose, a range of key water parameters were measured at eight stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM), and transparent exopolymer particles (TEP), which were all significantly elevated at the inshore compared the other seven sites. Shifts in the bacterial communities were specific to each sampled habitat. Two OTUs, belonging to the genera Escherichia/Shigella (Gammaproteobacteria) and Ralstonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes or OTUs within the sampled habitats. In addition, we observed very distinct communities between the investigated habitats. Our data show strong changes in the bacterial community composition at the inshore site for water column and sediment samples. Alarmingly, there was generally a high prevalence of potentially pathogenic bacteria across the entire gradient.

The production and quality of Rehmannia glutinosa can be dramatically reduced by replant disease under consecutive monoculture. The root-associated microbiome, also known as the second genome of the plant, was investigated to understand its impact on plant health. Culture-dependent and culture-independent pyrosequencing analysis was applied to assess the shifts in soil bacterial communities in the rhizosphere and rhizoplane under consecutive monoculture. The results show that the root-associated microbiome (including rhizosphere and rhizoplane microbiomes) was significantly impacted by rhizocompartments and consecutive monoculture. Consecutive monoculture of R. glutinosa led to a significant decline in the relative abundance of the phyla Firmicutes and Actinobacteria in the rhizosphere and rhizoplane. Furthermore, the families Flavobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae enriched while Pseudomonadaceae, Bacillaceae, and Micrococcaceae decreased under consecutive monoculture. At the genus level, Pseudomonas, Bacillus, and Arthrobacter were prevalent in the newly planted soil, which decreased in consecutive monocultured soils. Besides, culture-dependent analysis confirmed the widespread presence of Pseudomonas spp. and Bacillus spp. in newly planted soil and their strong antagonistic activities against fungal pathogens. In conclusion, R. glutinosa monoculture resulted in distinct root-associated microbiome variation with a reduction in the abundance of beneficial microbes, which might contribute to the declined soil suppressiveness to fungal pathogens in the monoculture regime.

Increased abundance of potentially pathogenic Vibrio and a marine heatwave co-occur with a Pacific Oyster summer mortality event