Bacterial Community Composition Research Articles

Simultaneous methane mitigation and nitrogen removal by denitrifying anaerobic methane oxidation in lake sediments

Methane (CH4) is a potent greenhouse gas, with lake ecosystems significantly contributing to its global emissions. Denitrifying anaerobic methane oxidation (DAMO) process, mediated by NC10 bacteria and ANME-2d archaea, links global carbon and nitrogen cycles. However, their potential roles in mitigating methane emissions and removing nitrogen from lake ecosystems remain unclear. This study explored the spatial variations in activities of nitrite- and nitrate-DAMO and their functional microbes in Changdanghu Lake sediments (Jiangsu Province, China). The results showed that although the average abundance of ANME-2d archaea (5.0 × 106 copies g−1) was significantly higher than that of NC10 bacteria (2.1 × 106 copies g−1), the average potential rates of nitrite-DAMO (4.59 nmol 13CO2 g−1 d−1) and nitrate-DAMO (5.01 nmol 13CO2 g−1 d−1) showed no significant difference across all sampling sites. It is estimated that nitrite- and nitrate-DAMO consumed approximately 6.46 and 7.05 mg CH4 m−2 d−1, respectively, which accordingly achieved 15.07–24.95 mg m−2 d−1 nitrogen removal from the studied lake sediments. Statistical analyses found that nitrite- and nitrate-DAMO activities were both significantly related to sediment nitrate contents and ANME-2d archaeal abundance. In addition, NC10 bacterial and ANME-2d archaeal community compositions showed significant correlations with sediment organic carbon content and water depth. Overall, this study underscores the dual roles of nitrite- and nitrate-DAMO processes in CH4 mitigation and nitrogen elimination and their key environmental impact factors (sediment organic carbon and inorganic nitrogen contents, and water depth) in shallow lake, enhancing the understanding of carbon and nitrogen cycles in freshwater aquatic ecosystems.

Soil microbial community responses to long-term experimental warming in an alpine Dryas octopetala heath in Norway

Over the last century, high-altitude and high-latitude regions have experienced global warming at rates higher than the worldwide average. Climate change influences complex soil-microbe-plant-atmosphere interactions, leading to changes in plant-associated soil microbial diversity and functioning and alterations in nutrient cycling, carbon fluxes, and storage. This study analyzed how two decades of global warming simulated by open-top chambers (OTCs) affected soil bacterial and fungal communities in an alpine dwarf-shrub heath dominated by Dryas octopetala in Norway. We collected soil samples from 10 OTCs and 10 control plots and compared their physicochemical properties, microbial biomass, extracellular enzyme activities, and bacterial and fungal community diversity and composition. Warming did not significantly affect the bacterial community despite the tendency to reduce alpha diversity and increase the degree of specialisation. In contrast, two decades of warming significantly affected fungal community composition, which was dominated by ectomycorrhizal Basidiomycota. While there was no significant effect on the total fungal community diversity, a significant shift in saprotrophic Ascomycota taxa was observed between the warmed and control plots. Their positive correlations with oxidative enzymes and fungal biomass suggest that long-term warming might lead to an increase in fungal biomass and the activity of oxidative enzymes, promoting the decomposition of more recalcitrant biopolymers. This may result in an increase in CO2 flux into the atmosphere and a decrease in ecosystem C storage.

Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities.

Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.

[Characterization of Microplastic Surface Bacterial Community Structure and Prediction of Ecological Risk in Poyang Lake, China].

In recent years, the environmental pollution of microplastics in Poyang Lake has received increasing attention. Baisha Lake of Poyang Lake was selected as the study area, and samples of water and sediments of Baisha Lake and the microplastics therein were collected, and the polymer types of microplastics were identified as polyethylene (PE), polyester (PET), polypropylene (PP), and polystyrene (PS) using Fourier infrared spectroscopy. We also analyzed the structural composition of bacterial communities in water, in sediments, and on microplastic surfaces using 16S high-throughput sequencing. The species richness and diversity of bacteria on the microplastic surfaces were lower than those in the surrounding water and sediments. The results of NMDS analysis showed that the bacterial community structures on the microplastic surfaces differed greatly from those in the surrounding sediments and water. The bacterial community composition in water and sediment differed from that on the microplastic surfaces, and the dominant bacterial phyla on the microplastic surfaces were Proteobacteria and Bacteroidota, and their relative abundance on the microplastic surfaces was higher than that in sediment. The relative abundance of Proteobacteria was higher than that in water. The relative abundances of Bacteroidota and Actinobacteriota were significantly lower than that of water. Massilia and Pseudomonas were the dominant genera on the microplastic surfaces, and their relative abundances were significantly higher than those in the surrounding water and sediments. BugBase phenotype prediction revealed that the relative abundance of contains mobile elements, biofilm formation, potential pathogenicity, and stress tolerance phenotypes of microplastic bacterial communities were significantly higher than those of the surrounding water and sediments. The results revealed that microplastics may have contributed to the spread of harmful bacteria, including pathogenic bacteria, and increased the potential pathogenicity of bacterial communities. Additionally, microplastic surface bacterial communities had higher phenotypes of mobile gene element content. Revealing the potential harm of microplastic pollution to wetland ecology at the micro level may provide a scientific reference for maintaining the ecological stability of wetlands.

[Bacterial Community Structure of Typical Lake Sediments in Yinchuan City and Its Response to Heavy Metals].

Lake wetlands are extremely important and special ecosystems, which are important for regional water resource storage, environmental protection, and biodiversity maintenance. Sediment bacteria are an important component of lake ecosystems and are a major driver of biogeochemical cycling in lakes. In order to investigate the community structure of bacteria in typical lake sediments in Yinchuan City and their influencing factors, three typical lakes in Yinchuan City (Yuehai Lake, Mingcui Lake, and Xiniu Lake) were selected for the study and surface sediments were collected in January, April, July, and October 2021. The composition of the sediment bacterial community was examined using 16S rDNA high-throughput sequencing technology, and the response relationships between them and heavy metals were explored. The results showed that the ecological hazard coefficient for heavy metals in the sediments of three typical lakes in Yinchuan City was far less than 40, and the ecological hazard index was far less than 150, all of which indicated a minor ecological hazard. There were no significant differences in bacterial community diversity among the three lakes, but there were significant variations in diversity among the lakes in different seasons and significant differences in community composition. The dominant phyla (top three in terms of relative abundance) in Yuehai Lake, Mingcui Lake, and Xiniu Lake were Proteobacteria, Bacteroidetes, and Chloroflexi. The dominant lower orders were Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The main divergent species that occurred at the phylum level in typical lakes in Yinchuan were Proteobacteria, Bacteroidetes, Euryarchaeota, Firmicutes, Actinobacteria, and Acidobacteria. The sediment bacterial community structure of Yuehai Lake was significantly correlated with Cu, Fe, Mn, Zn, As, and Pb; the sediment bacterial community structure of Lake Mingcui was significantly correlated with Fe, Pb, and Cr; and the sediment bacterial community structure of Xiniu Lake was not significantly correlated with heavy metals. The types and contents of sediment heavy metals had a significant effect on the bacterial community structure of sediments in Yinchuan Yuehai Lake and Mingcui Lake and were important environmental factors that caused changes in the bacterial community structure of lake sediments.

[Characteristics of Epiphytic Bacterial Community on Submerged Macrophytes in Water Environment Supplemented with Reclaimed Water].

Biofilms attached to submerged macrophytes play an important role in improving the water quality of the water environment supplemented with reclaimed water. In order to explore the effects of reclaimed water quality and submerged macrophyte species on the characteristics of an epiphytic bacterial community, different types of submerged macrophytes were selected as research objects in this study. 16S rRNA high-throughput sequencing technology was used on the epiphytic bacteria and the surrounding environmental samples to analyze the bacterial community structure and functional genes. The results showed that approximately 20%-35% of the nitrogen and phosphorus nutrients were absorbed and utilized in the water environment supplemented with reclaimed water. However, the COD, turbidity, and chroma of the downstream water were significantly increased. The bacterial community of the biofilms attached to submerged macrophytes was significantly different from that in the surrounding environment (soil, sediment, and water body) and in the activated sludge that was treated by reclaimed water. In terms of bacterial community diversity, the richness and diversity were significantly lower than those of soil and sediment but higher than those of plankton bacteria in water. In terms of bacterial community composition, dominant genera and corresponding abundances were also different from those of other samples. The main dominant bacterial genera were Sphingomonas, Aeromonas, Pseudomonas, and Acinetobacter, accounting for 7%-40%, respectively. Both macrophyte species and the quality of reclaimed water (BOD5, TN, NH4+-N, and TP) could affect the bacterial community. However, the effect of water quality of the bacterial community was greater than that of macrophytes species. Additionally, the quality of reclaimed water also affected the abundance of functional genes in the bacterial community, and the relative abundance of nitrogen and phosphorus cycling functional genes was higher in areas with higher nitrogen and phosphorus concentrations.

Analysis of chlorhexidine, antibiotics and bacterial community composition in water environments from Brazil, Cameroon and Madagascar during the COVID-19 pandemic

The widespread of chlorhexidine and antibiotics in the water bodies, which grew during the global COVID-19 pandemic, can increase the dispersion of antibiotic resistance. We assessed the occurrence of these pharmaceutical compounds as well as SARS-CoV-2 and analysed the bacterial community structure of hospital and urban wastewaters from Brazil, Cameroon, and Madagascar. Water and wastewater samples (n = 59) were collected between January–June 2022. Chlorhexidine, azithromycin, levofloxacin, ceftriaxone, gentamicin and meropenem were screened by Ultra-High-Performance Liquid Chromatography coupled with mass spectrometer. SARS-CoV-2 was detected based on the nucleocapsid gene (in Cameroon and Madagascar), and envelope and spike protein-encoding genes (in Brazil). The total community-DNA was extracted and used for bacterial community analysis based on the 16S rRNA gene. To unravel likely interaction between pharmaceutical compounds and/or SARS-CoV-2 with the water bacterial community, multivariate statistics were performed. Chlorhexidine was found in hospital wastewater effluent from Brazil with a maximum concentration value of 89.28 μg/L. Additionally, antibiotic residues such as azithromycin and levofloxacin were also present at concentrations between 0.32–7.37 μg/L and 0.11–118.91 μg/L, respectively. In Cameroon, azithromycin was the most found antibiotic present at concentrations from 1.14 to 1.21 μg/L. In Madagascar instead, ceftriaxone (0.68–11.53 μg/L) and levofloxacin (0.15–0.30 μg/L) were commonly found. The bacterial phyla statistically significant different (P < 0,05) among participating countries were Proteobacteria, Patescibacteria and Dependentiae which were mainly abundant in waters sampled in Africa and, other phyla such as Firmicutes, Campylobacterota and Fusobacteriota were more abundant in Brazil. The phylum Caldisericota was only found in raw hospital wastewater samples from Madagascar. The canonical correspondence analysis results suggest significant correlation of azithromycin, meropenem and levofloxacin with bacteria families such as Enterococcaceae, Flavobacteriaceae, Deinococcaceae, Thermacetogeniaceae and Desulfomonilaceae, Spirochaetaceae, Methanosaetaceae, Synergistaceae, respectively. Water samples were also positive for SARS-CoV-2 with the lowest number of hospitalized COVID-19 patients in Madagascar (n = 7) and Brazil (n = 30). Our work provides new data about the bacterial community profile and the presence of pharmaceutical compounds in the hospital effluents from Brazil, Cameroon, and Madagascar, whose limited information is available. These compounds can exacerbate the spreading of antibiotic resistance and therefore pose a risk to public health.

Evaluation of fate of organic matter in sediment through microcosm experiments

AbstractLaboratory microcosm experiments help to understand the degradation pattern of different sources derived from organic matter (OM) at the sediment–water interface and relate it to field processes. Microcosm experiments were carried out for 65 days to assess the degradation of organic materials such as diatoms, zooplankton, and mangrove leaves using source‐specific fatty acid (FA) biomarkers. The viable bacterial population in the microcosm sediment was low on day 1, but on day 3, it increased substantially by two to threefold in all the treatments. An increase in the bacterial population resulted in a decrease in the FAs specific to organic materials during the initial incubation phase (10 days), suggesting the degradation of organic materials derived from different sources. The FAs specific to diatoms showed faster degradation when compared to zooplankton and mangrove‐specific FAs. The degradation of FAs was influenced by the nature of the source material, unsaturation of FAs, and the sediment type. Sandy sediment facilitated higher degradation of diatom and zooplankton‐specific FAs, whereas mangrove‐specific FAs showed higher degradation in silty‐clay sediment. Thus, bacterial community composition coupled with the habitat characteristics, the OM composition, and the grain size of the sediment, influenced the degradation of FAs. The degradation of mangrove‐specific long‐chain FAs was ~1.11–2.5 times higher when spiked with plankton‐derived labile OM from mixed sources, which otherwise took a longer time for degradation pointing toward co‐metabolism (priming effect), which could play a significant role in the cycling of terrestrial plant‐derived OM in an estuarine ecosystem.

The composition and function of bacterial communities in Bombyx mori (Lepidoptera: Bombycidae) changed dramatically with infected fungi: A new potential to culture Cordyceps cicadae.

Cordyceps cicadae (Hypocreales: Cordycipitaceae) is a renowned entomopathogenic fungus used as herbal medicine in China. However, wild C. cicadae resources have been threatened by heavy harvesting. We hypothesised that Bombyx mori L. (Lepidoptera: Bombycidae) could be a new alternative to cultivate C. cicadae due to the low cost of rearing. Bacterial communities are crucial for the formation of Cordyceps and for promoting the production of metabolites. To better understand the bacterial community structure associated with Cordyceps, three Claviciptaceae fungi were used to explore the pathogenicity of the silkworms. Here, fifth-instar silkworms were infected with C. cicadae, Cordyceps cateniannulata (Hypocreales: Cordycipitaceae) and Beauveria bassiana (Hypocreales: Cordycipitaceae). Subsequently, we applied high-throughput sequencing to explore the composition of bacterial communities in silkworms. Our results showed that all three fungi were highly pathogenic to silkworms, which suggests that silkworms have the potential to cultivate Cordyceps. After fungal infection, the diversity of bacterial communities in silkworms decreased significantly, and the abundance of Staphylococcus increased in mummified larvae, which may play a role in the death process when the host suffers infection by entomopathogenic fungi. Furthermore, there were high similarities in the bacterial community composition and function in the C. cicadae and C. cateniannulata infected samples, and the phylogenetic analysis suggested that these similarities may be related to the fungal phylogenetic relationship. Our findings reveal that infection with different entomopathogenic fungi affects the composition and function of bacterial communities in silkworms and that the bacterial species associated with Cordyceps are primarily host dependent, while fungal infection affects bacterial abundance.

Comprehensive analysis of metal(loid)s and associated metal(loid) resistance genes in atmospheric particulate matter

Despite global concerns about metal(loid)s in atmospheric particulate matter (PM), the presence of metal(loid) resistance genes (MRGs) in PM remains unknown. Therefore, we conducted a comprehensive investigation of the metal(loid)s and associated MRGs in PMs in two seasons (summer and winter) in Xiamen, China. According to the geoaccumulation index (Igeo), most metal(loid)s, except for V and Mn, exhibited enrichment in PM, suggesting potential anthropogenic sources. By employing Positive Matrix Factorization (PMF) model, utilizing a dataset encompassing both total and bioaccessible metal(loid)s, along with backward trajectory simulations, traffic emissions were determined to be the primary potential contributor of metal(loid)s in summer, whereas coal combustion was observed to have a dominant contribution in winter. The major contributor to the carcinogenic risk of metal(loid)s in both summer and winter was predominantly attributed to coal combustion, which serves as the main source of bioaccessible Cr. Bacterial communities within PMs showed lower diversity and network complexity in summer than in winter, with Pseudomonadales being the dominant order. Abundant MRGs, including the As(III) S-adenosylmethionine methyltransferase gene (arsM), Cu(I)-translocating P-type ATPase gene (copA), Zn(II)/Cd(II)/Pb(II)-translocating P-type ATPase gene (zntA), and Zn(II)-translocating P-type ATPase gene (ziaA), were detected within the PMs. Seasonal variations were observed for the metal(loid) concentration, bacterial community structure, and MRG abundance. The bacterial community composition and MRG abundance within PMs were primarily influenced by temperature, rather than metal(loid)s. This research offers novel perspectives on the occurrence of metal(loid)s and MRGs in PMs, thereby contributing to the control of air pollution.

PSII-19 Fecal microbiota composition of weaned piglets under mixed management and poor housing conditions fed diets increased in threonine, methionine and tryptophan

Abstract This study evaluated the effects of increased dietary Thr, Met and Trp supplementation on fecal microbiota composition of weaned piglets raised under contrasting sanitary conditions [(GOOD SC) or under mixed management and poor housing conditions (MM+POOR SC)] during the nursery phase. A total of 144 entire male piglets [body weight (BW) = 6.33 ± 0.91 kg] from a high sanitary status (HSS) farm were randomly housed following a 2×2 factorial arrangement regarding BW blocks. Factorial arrangement was composed of two contrasting SC (GOOD or MM+POOR) and two diets [control, with nutritional requirements according to NRC (2012); or supplemented with Thr:Lys, Met+Cys:Lys and Trp:Lys 20% more than the control]. In total, 12 pens with three piglets each were used for treatment. On d -2, the 144 HSS piglets were allocated to one of two facilities under contrasting SCs. Also on d -2, to mimic a mixed management in the MM+POOR SC, 48 entire male piglets, from a commercial farm with low sanitary status (LSS), were randomly allocated by two piglets per pen into the same pens where the three HSS piglets were. On d 0, the two LSS piglets were removed from the HSS pens and allocated as sentinels into the remaining pens (four/pen) located between pens with HSS piglets. The MM+POOR SC had a weekly cleaning routine only to remove the manure located under the slatted floor, while in the GOOD SC, a daily cleaning routine and a high level of biosecurity protocol were adopted. One fecal sample per pen was collected on d 0, 21 and 42. The V4 region of the bacterial 16S rRNA gene was amplified from each fecal sample to evaluate ecological changes into bacterial communities and taxonomy. Mean relative abundance for each family/genus/species (taxon) across groups were depicted as a heatmap using the log2 transformed relative abundance of the most dominant taxa based on a 2% cutoff and network analysis of clusters of co-occurrences of the most relevant taxa (Figure 1). Overall, fecal microbiome analyses revealed no differences (P &amp;gt;0.05) in bacterial community composition and individual taxon abundances at the bacterial genus level across treatments over time. The alpha- and beta-diversity analysis showed no diet or SC differences (P &amp;gt;0.05). Additional community structure analysis based on co-occurrence network mapping revealed the absence of major temporal changes in architecture or keystone nodes (taxa) for HSS animals housed in either GOOD or MM+POOR SCs, despite the AA+ supplementation. The analysis revealed no specific taxon or taxa that were preferentially enriched or diminished over time (P &amp;gt; 0.05). According to our results, the microbial fecal composition of weaned piglets under GOOD or MM+POOR SCs measured using 16S rRNA sequencing analysis was stable including the major central taxa with no Thr, Met and Trp supplementation effect.

227 Comparative analysis of rumen bacterial communities from bison heifers fed two forage-based diets of different quality

Abstract Bison have a demonstrated ability to thrive on low-quality forage, an attribute that distinguishes them from their domestic ruminant counterparts. This could be attributed to the capability of their rumen symbiotic microorganisms in extracting more nutrients out of plant biomass. To gain further insight into the role of the bison microbiome in this beneficial adaptation, the primary objective of this study was to determine the diversity and composition of ruminal bacteria in bison fed poor versus good quality forage-based diets. Ruminal content was collected by stomach tubing from 25 bison heifers fed good quality forage (GQG) during the summer (last week of June 2023) at the McGinley Ranch (Gordon, Nebraska, USA). The same individuals were then transitioned to low quality hay (PQG) in pen confinement for approximately 4 to 5 wk before resampling. Data generated from Illumina MiSeq (2×300) sequencing of PCR amplicons targeting the V1-V3 region of the 16S rRNA gene were analyzed using a combination of custom Perl scripts, and publicly available software (Mothur v.1.40, RDP classifier and NCBI Blast). Principal Coordinate Analysis (PCoA) showed a clear distinction in bacterial composition between the two types of forages (Figure 1). Further analysis of species-level operational taxonomic units (OTUs) was performed, and a total of 78,808 OTUs were identified across all samples. From the 20 most highly represented OTUs, the respective abundance of twelve OTUs showed significant differences between the two forage types (Kruskal-Wallis’s sum-rank test; P &amp;lt; 0.05). For example, OTUs SD_Bb-00014 (µGQG = 1.06% vs µPQG = 0.19%), and SD_Bb-00049 (µGQG = 0.98% vs µPQG = 0.08%) showed significant decreases in abundance when animals switched to PQG. Conversely, OTUs SD_Bb-00071 (µGQG = 0.2% vs µPQG = 2.71%), SD_Bb-00049 (µGQG = 0.68% vs µPQG = 1.67%) and OTUs SD_Bb-00148 (µGQG = 0.19% vs µPQG = 1.40%) exhibited a significant increase in abundance in response to the forage transition. Notably, only one of the assessed OTUs, SD_Bb-00071, showed high sequence identity to its closest valid relative, Fibrobacter succinogenes (98.41%). In contrast, most of the other highly represented OTUs were found to be very dissimilar to known species, suggesting that they might represent novel or currently uncharacterized bacterial species (Table 1). Together, these results demonstrate the significant impact of variations in nutritional value and forage quality on the composition of rumen bacterial communities in the North American bison. Poor forage quality appeared to favor bacterial species such as Fibrobacter succinogenes, known for its cellulolytic capabilities, presumably because of its greater efficiency in breaking down more resistant plant cell walls. Its ability and that of other abundant OTUs to efficiently convert plant fibers into assimilable nutrients is likely critical in allowing bison to perform better on poor-quality forage compared with domesticated ruminants.

Bacterial community diversity, abundance, and composition of rearing water and red tilapia gills from open river cages and earthen ponds in Central Thailand

Bacterial community diversity, abundance, and composition of rearing water and red tilapia gills from open river cages and earthen ponds in Central Thailand

3D intrusions transport active surface microbial assemblages to the dark ocean

Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.

Exploring the impact of breast cancer on colonization resistance of mouse microbiota using network node manipulation

Breast cancer, a global health concern affecting women, has been linked to alterations in the gut microbiota, impacting various aspects of human health. This study investigates the interplay between breast cancer and the gut microbiome, particularly focusing on colonization resistance—an essential feature of the microbiota's ability to prevent pathogenic overgrowth. Using a mouse model of breast cancer, we employ diversity analysis, co-occurrence network analysis, and robustness tests to elucidate the impact of breast cancer on microbiome dynamics. Our results reveal that breast cancer exposure affects the bacterial community's composition and structure, with temporal dynamics playing a role. Network analysis demonstrates that breast cancer disrupts microbial interactions and decreases network complexity, potentially compromising colonization resistance. Moreover, network robustness analysis shows the susceptibility of the microbiota to node removal, indicating potential vulnerability to pathogenic colonization. Additionally, predicted metabolic profiling of the microbiome highlights the significance of the enzyme EC 6.2.1.2 - Butyrate--CoA ligase, potentially increasing butyrate, and balancing the reduction of colonization resistance. The identification of Rubrobacter as a key contributor to this enzyme suggests its role in shaping the microbiota's response to breast cancer. This study uncovers the intricate relationship between breast cancer, the gut microbiome, and colonization resistance, providing insights into potential therapeutic strategies and diagnostic approaches for breast cancer patients.

Mediterranean pine forest decline: A matter of root-associated microbiota and climate change

Forest ecosystems worldwide currently face worrying episodes of forest decline, which have boosted weakening and mortality of the trees. In the Mediterranean region, especially in the southeast Iberian Peninsula, Pinus sylvestris forests are severely affected by this phenomenon, and it has been commonly attributed to drought events. Remarkably, the role of root microbiota on pine decline has been overlooked and remains unclear. We therefore used metabarcoding to identify the belowground microbial communities of decline-affected and unaffected pine trees. Taxonomic composition of bacterial and fungal rhizosphere communities, and fungal populations dwelling in root endosphere showed different profiles depending on the health status of the trees. The root endosphere of asymptomatic trees was as strongly dominated by ‘Candidatus Phytoplasma pini’ as the root of decline-affected pines, accounting for >99 % of the total bacterial sequences in some samples. Notwithstanding, the titer of this phytopathogen was four-fold higher in symptomatic trees than in symptomless ones. Furthermore, the microbiota inhabiting the root endosphere of decline-affected trees assembled into a less complex and more modularized network. Thus, the observed changes in the microbial communities could be a cause or a consequence of forest decline phenomenon. Moreover, ‘Ca. Phytoplasma pini’ is positively correlated to Pinus sylvestris decline events, either as the primary cause of pine decline or as an opportunistic pathogen exacerbating the process once the tree has been weaken by other factors.

Cyanobacteria-green microalgae consortia enhance soil fertility and plant growth by shaping the native soil microbiome of Capsicum annuum

Alternative solutions to chemical fertilizers that can enhance soil fertility, increase crop yield, promote sustainable agriculture and reduce harmful environmental impacts are urgently required. Microalgal bio-inoculants can improve soil fertility, plant growth and crop yield, yet the response of native soil microbiome to microalgal application remains largely unexplored. A pot experiment was conducted to assess the effects of microalgae (a consortium of cyanobacteria and green microalgae) inoculation on the growth and yield of chili plant, soil fertility and soil microbiome. Our results showed that microalgal inoculation significantly enhanced plant morphometric parameters and increased dehydrogenase activity (p < 0.05). Similarly, soil organic carbon , soil chlorophyll , total polysaccharides and nutrients such as carbon , nitrogen , phosphorus , potassium and manganese were also significantly (p < 0.05) enriched in microalgal treatment groups (50% and 100%) compared to the control. Results showed that microalgal inoculation increased the soil microbial diversity, with the richness being higher in treated soils than control. Metagenomics analysis revealed a shift in bacterial and fungal community composition with firmicutes, chloroflexi, planctomycetes, proteobacteria, bacillariophyta, basidiomycota and glomeromycota dominating microalgal- treated soils, while actinobacteria, bacteroidetes, and streptomycota dominating control soils. The findings suggested that microalgal bio-inoculation can increase the diversity and composition of native soil microbiomes, enhance soil fertility, growth, and yield in chili plants.

Assessment of Soil Bacterial Community Compositions by Structural–Functional Genomics and Soil Edaphic Factors Largely Explain the Impact of Coal Mining

Assessment of Soil Bacterial Community Compositions by Structural–Functional Genomics and Soil Edaphic Factors Largely Explain the Impact of Coal Mining

The Influence of Forest Litter Characteristics on Bacterial and Fungal Community Diversity in the Picea crassifolia Ecosystem on the Qinghai–Tibet Plateau

The biodiversity and activity of microorganisms are crucial for litter decomposition, but how litter traits at different stages of decomposition drive changes in microbial communities has yet to be thoroughly explored. In the typical alpine hilly area of the Qinghai–Tibet Plateau, three types of litter at different decomposition stages were selected under a natural Picea crassifolia (Picea crassifolia Kom.) forest: undecomposed (A-1), partially decomposed (A-2), and fully decomposed (A-3). By measuring physicochemical indicators, microbial diversity, and the composition of the litter at different decomposition stages, this study investigates the community changes and responses of bacteria to litter characteristic changes at different decomposition levels. The results show that with the increase in decomposition level, bacterial diversity increases, community structure changes, and network complexity gradually increases, while the changes in fungal communities are insignificant. Structural equation modeling indicates that the first principal component (PC1) of litter properties is significantly negatively correlated with bacterial diversity and positively correlated with bacterial community composition. There is no significant correlation between fungal diversity and community composition, indicating a closer relationship between bacteria and litter characteristics than fungi. In summary, with an increase in litter decomposition level, the diversity and network complexity of bacterial and fungal communities will significantly increase, which is related to the changes in various litter characteristics. This study provides a scientific basis for the regulatory mechanism of litter decomposition and turnover in the alpine hilly area of the Qinghai–Tibet Plateau, specifically in Picea crassifolia forests.

Tomato domestication rather than subsequent breeding events reduces microbial associations related to phosphorus recovery

Legacy phosphorus (P) is a reservoir of sparingly available P, and its recovery could enhance sustainable use of nonrenewable mineral fertilizers. Domestication has affected P acquisition, but it is unknown if subsequent breeding efforts, like the Green Revolution (GR), had a similar effect. We examined how domestication and breeding events altered P acquisition by growing wild, traditional (pre-GR), and modern (post-GR) tomato in soil with legacy P but low bioavailable P. Wild tomatoes, particularly accession LA0716 (Solanum pennellii), heavily cultured rhizosphere P solubilizers, suggesting reliance on microbial associations to acquire P. Wild tomato also had a greater abundance of other putatively beneficial bacteria, including those that produce chelating agents and antibiotic compounds. Although wild tomatoes had a high abundance of these P solubilizers, they had lower relative biomass and greater P stress factor than traditional or modern tomato. Compared to wild tomato, domesticated tomato was more tolerant to P deficiency, and both cultivated groups had a similar rhizosphere bacterial community composition. Ultimately, this study suggests that while domestication changed tomato P recovery by reducing microbial associations, subsequent breeding processes have not further impacted microbial P acquisition mechanisms. Selecting microbial P-related traits that diminished with domestication may therefore increase legacy P solubilization.