Search Results (18)

Global climate change and invasive plants significantly impact biodiversity and ecosystem functions. This study focuses on the effects of progressive warming on microbial communities within the Solidago canadensis invasion community, simulated through six stages of invasion progression, from minimal to dominant S. canadensis presence alongside native Artemisia argyi, in bulk soils collected from a natural habitat and cultivated under controlled greenhouse conditions. Utilizing high-throughput sequencing and microbial community analysis on 72 samples collected from the S. canadensis invasion community, the shifts in soil microbiota under varying warming scenarios were investigated (+0 °C, +1.15 °C and +1.86 °C). We observed significant shifts in invasion community soil bacteria in response to warming, with Acidobacteria, Actinobacteria, and others showing distinct responses between baseline and warmed conditions, while groups like Chlorobi and Cyanobacteria only differed significantly at higher temperature extremes. The random forests algorithm identified 14 taxa as biomarkers and a model was established to correlate S. canadensis invasion community soil microbiota with progressive warming. Co-occurrence network analysis revealed that moderate warming enhances microbial connectivity and the presence of a super-generalist, ASV 1160. However, further warming disrupts these networks by eliminating key generalists, revealing a potential reduction in network stability and diversity. These findings illuminate the dynamic responses of microbes in S. canadensis invasion community soil to varying temperature regimes, suggesting a model for successional dynamics and offering a deeper comprehension of microbial community shifts amid climatic fluctuations. This study delineates how warming significantly reshapes the soil microbial composition, potentially impacting S. canadensis’s invasion success unfavorably, thereby highlighting the importance of considering microbial dynamics in ecological management. Full article

Plants significantly shape root-associated microbiota, making rhizosphere microbes useful environmental indicator organisms for safety assessment. Here, we report the pyrosequencing of the bacterial 16S ribosomal RNA in rhizosphere soil samples collected from transgenic cry1Ab/cry1Ac Bt rice Huahui No. 1 (GM crop) and its parental counterpart, Minghui63. We identified a total of 2579 quantifiable bacterial operational taxonomic units (OTUs). Many treatment-enriched microbial OTUs were identified, including 14 NonGM-enriched OTUs and 10 GM-enriched OTUs. OTUs belonging to the phyla Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Nitrospirae, Chlorobi and GN04 were identified as statistically different in abundance between GM and the other two treatments. Compared with the different impacts of different rice varieties on microbiota, the impact of rice planting on microbiota is more obvious. Furthermore, Huahui No. 1 transgenic Bt rice had a greater impact on the rhizosphere bacterial communities than Minghui63. Early developmental stages of the transgenic Bt rice had a significant impact on many Bacillaceae communities. Soil chemical properties were not significantly altered by the presence of transgenic Bt rice. The peak concentration level of Bt protein products was detected during the seedling stage of transgenic Bt rice, which may be an intriguing factor for bacterial diversity variations. Based on these findings, we conclude that transgenic Bt rice has a significant impact on root-associated bacteria. This information may be leveraged in future environmental safety assessments of transgenic Bt rice varieties. Full article

With the development of modern aquaculture, the number of pathogenic bacteria in fish farms has gradually risen. Studies have shown that traditional Chinese medicinal herbs and natural products have greatly contributed to reducing bacterial growth and reproduction. To explore the changes in different proportions of Houttuynia cordata Thunb and Jussiaea stipulacea on the bacterial composition in water, roots, and sediments, we conducted 16S rRNA gene sequencing on samples of the same to analyze floating beds (60% H. cordata Thunb and 30% H. cordata Thunb, 30% J. stipulacea named HcT1, HcT2, and Jr, respectively) after 30 days in the presence of tilapia culture water, roots, and sediments with bacterial community changes in the respective experimental groups. The results showed that 4811 bacterial operational taxonomic units (OTUs) were obtained; the alterations included decreased Spirochaetae, Nitrospirae, and Elusimicrobia in water; a significant increase in Tenericutes, Chlorobi, and Nitrospirae in HcT1 roots; and decreased Firmicutes and Fusobacteria in HcT2 and Jr roots. Actinobacteria, Nitrospirae, Tenericutes, and Chlamydiae increased in the HcT1 sediment; Fusobacteria and Fibrobacteres increased in the HcT2 sediment; and Cyanobacteria, Gemmatimonadetes, and Acidobacteria increased in the Jr sediment. H. cordata Thunb decreased Tenericutes and Deferribacteres, while Chlorobi, Nitrospirae, and Gemmatimonadetes increased with a 60% planting area, whereas Actinobacteria and Cyanobacteria increased with a 30% planting area, and Jr only increased Fusobacteria and Fibrobacteres. When planting with herbs, Proteobacteria increased, while Deferribacteres and Elusimicrobia decreased. The pathogenic genera may transfer among the water, plant roots, and sediments, and floating cultivation with herbs may be beneficial for blocking the spread of the pathogenic genera found in the samples. Full article

Neurodevelopment is influenced by complex interactions between environmental factors, including social determinants of health (SDOH), nutrition, and even the microbiome. This longitudinal cohort study of 142 infants tested the hypothesis that microbial activity modulates the effects of nutrition on neurodevelopment. Salivary microbiome activity was measured at 6 months using RNA sequencing. Infant nutrition was assessed longitudinally with the Infant Feeding Practices survey. The primary outcome was presence/absence of neurodevelopmental delay (NDD) at 18 months on the Survey of Wellbeing in Young Children. A logistic regression model employing two microbial factors, one nutritional factor, and two SDOH accounted for 33.3% of the variance between neurodevelopmental groups (p < 0.001, AIC = 77.7). NDD was associated with Hispanic ethnicity (OR 18.1, 2.36–139.3; p = 0.003), no fish consumption (OR 10.6, 2.0–54.1; p = 0.003), and increased Candidatus Gracilibacteria activity (OR 1.43, 1.00–2.07; p = 0.007). Home built after 1977 (OR 0.02, 0.001–0.53; p = 0.004) and Chlorobi activity (OR 0.76, 0.62–0.93, p = 0.001) were associated with reduced risk of NDD. Microbial alpha diversity modulated the effect of fish consumption on NDD (X² = 5.7, p = 0.017). These data suggest the benefits of fish consumption for neurodevelopment may be mediated by microbial diversity. Confirmation in a larger, randomized trial is required. Full article

Fertile Chernozems of Southern Russia are of great value, so it is important to study the impact of agricultural activities on the soil quality. Changes in taxonomic composition and α-diversity of microbial communities of agricultural soils occupied by pea (Pisum sativum L.) and chickpea (Cicer arietinum L.) in response of cropland management were studied. A field experiment was conducted under four different conditions: (1) control, (2) mineral fertilizers (NPK) application alone, (3) pesticides application alone, and (4) fertilization combined with pesticides. The taxonomic composition of the soil bacterial community was studied by amplification and sequencing of the 16S rRNA gene. The predominance of Actinobacteria (17.7–32.3%), Proteobacteria (17.7–28.2%), Planctomycetes (10.1–21.3%), Acidobacteria (5.3–11.1%), Chloroflexi (1.0–7.1%), Gemmatimonadetes (2.5–8.0%), Bacteroidetes (3.6–11.3%), and Verrucomicrobia (3.9–9.2%) was noted. Introduction of pesticides led to an increase in the relative abundance of Chlorobi and Gemmatimonadetes. The time of sampling was the main significant factor determining the differences in the structure of soil microbial communities. All treatments did not have a significant effect on the α-diversity of the studied soils. Thus, treatment with mineral fertilizers and pesticides does not have a significant negative effect on the bacterial community of cultivated soils. Full article

The damaging competition between crops and parasitic weeds has a negative impact on agricultural productivity; however, the impact of disturbance on the soil’s microbial community has received less attention. Hence, this study investigates the microbial composition and diversity of the maize rhizosphere infected with Striga hermonthica using a shotgun sequencing approach from two maize-growing fields (Eruwa, Nigeria and Mbuzini, South Africa). The rhizosphere soil DNA was extracted from infested soil using a Nucleospin soil genomic DNA extraction kit and sequenced on an Illumina platform. The dominant phyla were Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Acidobacteria, Chloroflexi, Cyanobacteria, Planctomycetes, Verrucomicrobia, Chlorobi, Proteobacteria, Firmicutes, Nitrospirae, Thermotogae, Synergistetes, Ascomycota, Euryarchaeota, and Crenarchaeota. Bacteria phyla were observed to be of higher proportion in the rhizosphere soil samples obtained from Striga-infested maize field in Eruwa (Es) than those recovered from Mbuzini (Ms). The alpha diversity of microbial communities indicated insignificance differences (p > 0.05) between the five taxonomical groups (phylum, class, order, family, and genus), while the beta diversity produced a significant (p = 0.01, R = 0.52) difference in the microbial diversity of the infested soil. In summary, the study sheds light on the diversity and composition of the microbiome of Striga hermonthica-infested soil, which influences the microbial functions in the management and sustenance of plant health against parasitic weeds. Full article

To determine the reasonable rate of straw return and nitrogen (N) fertilizer use which may maintain soil ecosystem health, we analyzed their soil microbial biomass and composition in a 10-year field experiment with different rates of straw return (50%, 100%) and N fertilizer (270, 360, 450, 540 kg N ha⁻¹ yr⁻¹) by phospholipid fatty acid (PLFA) analysis and high-throughput sequencing. A rate of 50% straw return combined with 450 or 540 kg N ha⁻¹ yr⁻¹ effectively increased the soil available nutrient contents mainly for total nitrogen, available potassium, and available phosphorus. Total PLFAs indicated that straw return combined with N fertilizer promoted soil microbial growth and increased biomass. A rate of 100% straw return with 450 kg N ha⁻¹ yr⁻¹ was not conducive to the stability of the soil ecosystem according to the ratio of fungi to bacteria (F:B). The similar rate of straw returning and the similar level of nitrogen fertilizer application will be divided into the same cluster using a heatmap analysis. Some saprophytic fungi or pathogens became the dominant fungi genera, such as Gibberella, Sarocladium, Pseudallescheria, and Mycosphaerella, in the treatments with 100% straw returning combining higher N fertilizer (>450 kg ha⁻¹ yr⁻¹ yr⁻¹ added). The relative abundances of some heavy metal-tolerant bacteria, such as those in Proteobacteria and Chlorobi, increased in the soils in the 100% straw return treatments. Therefore, the combined application of 100% straw returning and higher N fertilizer (>450 kg ha⁻¹ yr⁻¹) added long-term was not appropriate for soil health, which will lead to the risk of disease and pollution in soil. Full article

Group B Streptococcus (GBS) colonizes the vaginal and rectal mucosa in a substantial proportion of healthy women, and GBS is a risk factor for GBS-associated adverse birth outcomes, such as bacterial infection, in neonates. Whether changes in the gut microbiota of GBS-infected pregnant women are associated with maternal complete blood cell count (CBC) and neonatal blood-gas analysis is unknown. To explore the relationship between the intestinal microecological composition of pregnant women and maternal blood routine and neonatal blood-gas analysis, we collected intestinal microecology samples of 26 pregnant women in clinic. They were divided into a positive group(GBS positive,GBS +) and a negative group (GBS negative, GBS-), with 12 in the positive group and 14 in the negative group. 16S rRNA gene sequencing was used to examine the gut microbiota profile from a fecal sample of pregnant women. CBC was carried out in enrolled pregnant women and umbilical arterial blood-gas analysis (UABGA)was conducted for analysis of intestinal microbiota composition, maternal blood routine and neonatal blood gas. Our results showed significant differences in the total number of organisms and microbial diversity of intestinal microbiota between healthy pregnant women and GBS-positive pregnant women. Particularly, abundances of Lentisphaerae, Chlorobi, Parcubacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria, Fusobacteria and Fibrobacteres were only detected in participants with GBS colonization. Blood-gas analysis revealed that neonates born to mothers with GBS colonization had significantly higher fractions of carboxyhemoglobin (FCOHb) and lower methemoglobin (FMetHb), and abundances of OTU80, OTU122, OTU518 and OTU375 were associated with blood-gas indicators, such as carboxyhemoglobin, methemoglobin, PCO2, PH and ABE. Interestingly, there were significant correlations between OTU levels and inflammatory indexes in pregnant women with GBS infection. Together, this study revealed for the first time that altered gut microbiota compositions are related to the inflammatory state in GBS-positive pregnant women and neonatal blood-gas indicators. GBS colonization may lead to significant changes in the gut microbiome, which might be involved in the pathogenesis of the maternal inflammatory state and neonatal blood gas abnormalities. Full article

Evolutionary relationships amongst Chlorobia and Ignavibacteria species/strains were examined using phylogenomic and comparative analyses of genome sequences. In a phylogenomic tree based on 282 conserved proteins, the named Chlorobia species formed a monophyletic clade containing two distinct subclades. One clade, encompassing the genera Chlorobaculum, Chlorobium, Pelodictyon, and Prosthecochloris, corresponds to the family Chlorobiaceae, whereas another clade, harboring Chloroherpeton thalassium, Candidatus Thermochlorobacter aerophilum, Candidatus Thermochlorobacteriaceae bacterium GBChlB, and Chlorobium sp. 445, is now proposed as a new family (Chloroherpetonaceae fam. nov). In parallel, our comparative genomic analyses have identified 47 conserved signature indels (CSIs) in diverse proteins that are exclusively present in members of the class Chlorobia or its two families, providing reliable means for identification. Two known Ignavibacteria species in our phylogenomic tree are found to group within a larger clade containing several Candidatus species and uncultured Chlorobi strains. A CSI in the SecY protein is uniquely shared by the species/strains from this “larger Ignavibacteria clade”. Two additional CSIs, which are commonly shared by Chlorobia species and the “larger Ignavibacteria clade”, support a specific relationship between these two groups. The newly identified molecular markers provide novel tools for genetic and biochemical studies and identification of these organisms. Full article

L-asparaginase (L-ASNase) is a biotechnologically relevant enzyme for the pharmaceutical, biosensor and food industries. Efforts to discover new promising L-ASNases for different fields of biotechnology have turned this group of enzymes into a growing family with amazing diversity. Here, we report that thermophile Melioribacter roseus from Ignavibacteriae of the Bacteroidetes/Chlorobi group possesses two L-ASNases—bacterial type II (MrAII) and plant-type (MrAIII). The current study is focused on a novel L-ASNase MrAII that was expressed in Escherichia coli, purified and characterized. The enzyme is optimally active at 70 °C and pH 9.3, with a high L-asparaginase activity of 1530 U/mg and L-glutaminase activity ~19% of the activity compared with L-asparagine. The kinetic parameters K_M and V_max for the enzyme were 1.4 mM and 5573 µM/min, respectively. The change in MrAII activity was not significant in the presence of 10 mM Ni²⁺, Mg²⁺ or EDTA, but increased with the addition of Cu²⁺ and Ca²⁺ by 56% and 77%, respectively, and was completely inhibited by Zn²⁺, Fe³⁺ or urea solutions 2–8 M. MrAII displays differential cytotoxic activity: cancer cell lines K562, Jurkat, LnCap, and SCOV-3 were more sensitive to MrAII treatment, compared with normal cells. MrAII represents the first described enzyme of a large group of uncharacterized counterparts from the Chlorobi-Ignavibacteriae-Bacteroidetes clade. Full article

The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences. Full article

In this study, a spatial model has been developed to investigate the role of water temperature to the distribution of bacteria over the selected regions in the Bay of Bengal, located in the southern region of Bangladesh using next-generation sequencing. Bacterial concentration, quantitative polymerase chain reactions, and sequencing were performed on water samples and identified Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, Planctomycetes, Proteobacteria, and Verrucomicrobia. The spatial model tessellated the parts of the Bay of Bengal with hexagons and analyzed the relationship between the distribution of bacteria and water temperature. A geographically weighted regression was used to observe whether water temperature contributed strongly or weakly to the distribution of bacteria. The residuals were examined to assess the model’s fitness. The spatial model has the potential to predict the bacterial diversity in the selected regions of Bangladesh. Full article

Photosynthesis is a key process for the establishment and maintenance of life on earth, and it is manifested in several major lineages of the prokaryote tree of life. The evolution of photosynthesis in anoxygenic photosynthetic bacteria is of major interest as these have the most ancient roots of photosynthetic systems. The phylogenetic relations between anoxygenic phototrophic bacteria were compared on the basis of sequences of key proteins of the type-II photosynthetic reaction center, including PufLM and PufH (PuhA), and a key enzyme of bacteriochlorophyll biosynthesis, the light-independent chlorophyllide reductase BchXYZ. The latter was common to all anoxygenic phototrophic bacteria, including those with a type-I and those with a type-II photosynthetic reaction center. The phylogenetic considerations included cultured phototrophic bacteria from several phyla, including Proteobacteria (138 species), Chloroflexi (five species), Chlorobi (six species), as well as Heliobacterium modesticaldum (Firmicutes), Chloracidobacterium acidophilum (Acidobacteria), and Gemmatimonas phototrophica (Gemmatimonadetes). Whenever available, type strains were studied. Phylogenetic relationships based on a photosynthesis tree (PS tree, including sequences of PufHLM-BchXYZ) were compared with those of 16S rRNA gene sequences (RNS tree). Despite some significant differences, large parts were congruent between the 16S rRNA phylogeny and photosynthesis proteins. The phylogenetic relations demonstrated that bacteriochlorophyll biosynthesis had evolved in ancestors of phototrophic green bacteria much earlier as compared to phototrophic purple bacteria and that multiple events independently formed different lineages of aerobic phototrophic purple bacteria, many of which have very ancient roots. The Rhodobacterales clearly represented the youngest group, which was separated from other Proteobacteria by a large evolutionary gap. Full article

The anaerobic ammonium oxidation (anammox) reaction removes nitrogen from wastewater, the performance of which is influenced by Ca²⁺; however, the effect of Ca²⁺ on microbial community structure is unclear. Therefore, the effects of Ca²⁺ concentration on the treatment performance of an anammox reactor and microbial community structure of anammox sludge were investigated. Ca²⁺ concentration minimally influenced the removal efficiency of NO₂⁻–N and NH₄⁺–N, but substantially influenced total N removal. Changing the Ca²⁺ concentration (between 25 and 125 mg/L) caused the average removal rate of total nitrogen to fluctuate by 3.3 percentage points. There were five major bacterial phyla in the anammox sludge: Proteobacteria, Chloroflexi, Acidobacteria, Planctomycete, and Chlorobi. Microbiological analysis revealed that the genera Acidobacterium, Anaerolinea, and Denitratisoma were positively correlated with Ca²⁺ concentration, and improved treatment performance of the anammox reactor. Moreover, uncultured Chlorobi bacterium clone RUGL1-218 (GQ421108.1) and uncultured sludge bacterium A21b (KT182572.1) may be key microorganisms for the immobilization of anammox bacteria. These findings offer a theoretical basis for improved wastewater treatment using the anammox process. Full article

In the vast majority of fossils, the organic matter is degraded with only an impression or cast of the organism remaining. In rare cases, ideal burial conditions result in a rapid fossilisation with an exceptional preservation of soft tissues and occasionally organic matter. Such deposits are known as Lagerstätten and have been found throughout the geological record. Exceptional preservation is often associated with finely crystalline quartz (e.g., cherts), fine sediments (e.g., muds) or volcanic ashes. Other mechanisms include burial in anoxic/euxinic sediments and in the absence of turbidity or scavenging. Exceptional preservation can also occur when an organism is encapsulated in carbonate cement, forming a concretion. This mechanism involves complex microbial processes, resulting in a supersaturation in carbonate, with microbial sulfate reduction and methane cycling the most commonly suggested processes. In addition, conditions of photic zone euxinia are often found to occur during concretion formation in marine environments. Concretions are ideal for the study of ancient and long-extinct organisms, through both imaging techniques and biomolecular approaches. These studies have provided valuable insights into the evolution of organisms and their environments through the Phanerozoic and have contributed to increasing interest in fields including chemotaxonomy, palaeobiology, palaeoecology and palaeophysiology. Full article