Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

SummaryTo quantify the major environmental drivers of stream bacterial population dynamics, we modelled temporal differences in stream bacterial communities to quantify community shifts, including those relating to cyclical seasonal variation and more sporadic bloom events. We applied Illumina MiSeq 16S rRNA bacterial gene sequencing of 892 stream biofilm samples, collected monthly for 36‐months from six streams. The streams were located a maximum of 118 km apart and drained three different catchment types (forest, urban and rural land uses). We identified repeatable seasonal patterns among bacterial taxa, allowing their separation into three ecological groupings, those following linear, bloom/trough and repeated, seasonal trends. Various physicochemical parameters (light, water and air temperature, pH, dissolved oxygen, nutrients) were linked to temporal community changes. Our models indicate that bloom events and seasonal episodes modify biofilm bacterial populations, suggesting that distinct microbial taxa thrive during these events including non‐cyanobacterial community members. These models could aid in determining how temporal environmental changes affect community assembly and guide the selection of appropriate statistical models to capture future community responses to environmental change.

Spatial patterns of bacterial community composition often follow a distance-decay relationship in which community dissimilarity increases with geographic distance. Such a relationship has been commonly observed in natural environments, but less so in engineered environments. In this study, bacterial abundance and community composition in filter media samples (n = 57) from full-scale rapid biofilters at 14 water treatment facilities across North America were determined using quantitative polymerase chain reaction and Illumina HiSeq high-throughput sequencing targeting the 16S rRNA gene, respectively. Bacteria were abundant on the filter media (108.8±0.3 to 1010.7±0.2 16S rRNA gene copies/cm3 bed volume) and the bacterial communities were highly diverse (Shannon index: 5.3±0.1 to 8.4±0.0). Significant inter-filter variations in bacterial community composition were observed, with weighted UniFrac dissimilarity values following a weak but highly significant distance-decay relationship (z = 0.0057±0.0006; P = 1.8 × 10-22). Approximately 50% of the variance in bacterial community composition was explained by the water quality parameters measured at the time of media sample collection (i.e. pH, temperature and dissolved organic carbon concentration). Overall, this study suggested that the microbiomes of biofilters are primarily shaped by geographic location and local water quality conditions but the influence of these factors on the microbiomes is tempered by filter design and operating conditions.

Net cage aquaculture alters the co-occurrence network and functions of bacterial communities in offshore areas

In eutrophic lakes, heterotrophic bacteria are closely associated with algal detritus and play a crucial role in nutrient cycling. However, the seasonal and spatial dynamics of free‐living (FL) and particle‐attached (PA) bacteria and the environmental factors shaping this relationship remain poorly understood. To address this issue, we explored the spatiotemporal patterns of bacterial community composition (BCC) in Lake Taihu, China, using terminal restriction fragment length polymorphism (T‐RFLP) and 454‐tag pyrosequencing of 16S rRNA gene. We generated a total of 218,027 high quality non‐cyanobacterial sequence reads that resulted in 4940 OTUs (97% cutoff), with Actinobacteria, β‐ and α‐proteobacteria being the predominant taxa. Although PA communities contained significantly higher alpha‐diversity than FL ones, we found that 59% of OTUs, that accounted for 96% of the total reads, were shared by both communities. The high degree of overlap between FL and PA communities indicates a high rate of dispersal potential, highlighting an underestimated connectivity and potentially similar ecological role for these two components. Distinct seasonal trends were recorded in both FL and PA communities, while spatial differences in BCC were small. In addition, both FL and PA bacterial communities exhibited similar patterns and synchrony, correlated to water temperature, nitrate and total suspended solids (TSS). Accordingly, the effects of eutrophication and hydrodynamics on the phylogenetic overlap and diversity between FL and PA communities were discussed.

Microbial communities play critical roles in ecosystem functioning across a wide range of environmental conditions. The physiological stress imposed by temperature, pH and resource levels can shape the structure and function of microbial communities; however, while often tested independently, factors influencing physiological stress on a community rarely occur in isolation from each other. Controlled experiments simultaneously testing multiple interactive stressors allow researchers to better assess the dynamical responses of microbial communities to rapidly changing environments. Using a full factorial, controlled experiment, we tested three hypotheses for how independent and interactive effects of abiotic stresses impact bacterial community composition, structure and function in a model system. We utilised an aquatic, pitcher plant-associated bacterial community in which microbial nutrient cycling is essential to the host plant and ecosystem. Temperature, pH and resource (food) concentration had strong independent and interactive effects on bacterial community composition, structure and function. Community functions did not respond to interactive stressors in the same way. Chitinase and protease enzymatic activities had opposite responses to temperature and pH changes, indicating that diverse functional measures are necessary for understanding the varied effects of interacting stressors. The most extreme abiotic stress combination (high temperature, lowest pH and excess food) resulted in the lowest enzyme activity and reduced species richness as compared to the other treatments. Stressful conditions, especially high temperature, strengthened correlations between community structure and function. Higher phylogenetic dispersion under abiotic extremes suggested selection for diverse taxa adapted to similar conditions through convergent evolution. These interactive effects highlight the often greater-than-additive impact of multiple stressors and demonstrate that environmental filtering and trait convergence shape microbial responses to stress.

In order to clarify the effects of mixture intercropping on the control of rice blast and the structure and function of the rhizosphere bacterial community, the 16S rRNA sequencing analysis of bacteria in rhizosphere soil of the selected high control efficiency (E=54.48%) (Shanyou 63/Huangkenuo) and low control efficiency (E=14.12%) combinations (Hexi 39/Huangkenuo) under the intercropping and monoculture treatments were performed with Illumina Hiseq sequencing technology. The results showed that soil bacteria, from 37 phyla, 116 classes, 244 orders, 384 families, 689 genera, were obtained in the intercropping system. Chloroflexi, Proteobacteria, and Actinobacteriota were the dominant bacterial groups. The relative abundance was higher than 15%. Alpha diversity analysis discovered that high-efficacy combination significantly increased the Shannon index and Chao1 index of rice rhizosphere bacterial community in intercropping conditions (<italic>P</italic>&lt;0.05), whereas there was no difference at <italic>P</italic>&gt;0.05 in low-efficiency combination. ANOSIM and PCoA analyses revealed that there was significant difference in the structure of the species in the rhizosphere bacterial community in monoculture (<italic>r </italic>= 0.48, <italic>P</italic>&lt;0.01), but no significant difference in the rhizosphere bacterial community structure between the high- and low-efficiency combinations following intercropping (<italic>P</italic>&gt;0.05), which indicating that intercropping increased the similarity of bacterial community structure between both combinations. Comparison to monoculture, the dominant bacterial group composition proved that the relative abundance of Shanyou63 Acidobacteriota decreased significantly, while the relative abundance of Shanyou 63 Actinobacteriota and Firmicutes increased significantly, but there was no significant difference among the dominant bacteria in Huangkenuo. Hexi 39 rhizosphere Patescilbacteria exhibited the significant decrease in low-efficiency combinations, whereas Gemmatimonadota showed the significant increase. PICRUSt2 function prediction discovered that the relative abundance of biosynthesis of other secondary metabolites in the main cultivars decreased significantly in the intercropping system, while the relative abundance of transcription, metabolism of cofactors and vitamins in intercropping cultivars increased significantly. In conclusion, to increase plant disease resistance and to provide data support for the theory of diverse intercropping for disease control, the high-efficacy combination had the ability to improve the diversity of rice rhizosphere bacteria and the structure and function of bacterial community by mixture intercropping, which effectively reduced the occurrence of rice blast and provided an application pathway for the improvement of soil microorganisms.

Marian Cove is experiencing some of the most rapid environmental changes in the Antarctic region; however, little is known about the response of bacterial communities to these changes. The main purpose of this study was to investigate the spatial variation of physical–biogeochemical–bacterial community features in the Marian Cove surface waters and the environmental parameters governing the spatial variation in the bacterial community composition during the summer of 2018. The Marian Cove surface waters are largely composed of two different characteristics of water masses: relatively low-temperature, -salinity, and -nutrient surface glacier water (named SGW) and relatively high-temperature, -salinity, and -nutrient surface Maxwell Bay water (named SMBW). The SGW bacterial communities were dominated by unclassified Cryomorphaceae, Sedimenticola, and Salibacter genera, while the SMBW bacterial communities were dominated by Sulfitobacter, Arcobacter, and Odoribacter genera. Spatial variations in bacterial community composition were mainly attributed to physical and biogeochemical characteristics, suggesting that the bacterial community composition of the Marian Cove surface waters is mainly determined by environmental characteristics. These findings provide a foundation to improve the understanding of bacterial community variations in response to a rapidly changing Marian Cove in the Antarctic.

The Mu Us Sandy Land represents a typical region for ecological restoration in China, characterized by the development of diverse landscapes including desert, meadow patches, arbor forests, and mixed arbor-shrub forests. This study aimed to investigate the diversity, composition, and differential taxa of soil bacterial communities across these distinct geographical landscapes, thereby elucidating the driving mechanisms of vegetation restoration on the sandy land soil microbiome. Soil samples were collected from four typical landscapes in the Mu Us Sandy Land: desert (B), meadow patch (D), arbor forest (T), and mixed arbor-shrub forest (C). High-throughput sequencing of the 16S rRNA gene was performed using the Illumina NextSeq 2000 platform. Our results revealed distinct patterns of bacterial community composition: Actinobacteria dominated the desert (37.42%), while Proteobacteria were more abundant in meadow patches and mixed arbor-shrub forests, and Bacillota were significantly enriched in arbor forests (20.32%). Beta diversity analysis combined with the ANOSIM test (R = 0.7168, P = 0.001) revealed significant divergence in bacterial community structure among the different landscapes. LEfSe analysis further identified specific biomarkers for each landscape, such as Rubrobacter and Streptomyces in the desert, and taxa associated with Acidobacteria and Proteobacteria in the mixed arbor-shrub forests. The research demonstrates that the different geographical landscapes in the Mu Us Sandy Land shape distinct soil bacterial communities. The mixed arbor-shrub forest exhibited a more complex community structure compared to the pure arbor forest, indicating its potential as a more sustainable and resilient ecological restoration model. These findings provide a baseline understanding of microbial community shifts associated with vegetation restoration, which may inform future studies integrating soil physicochemical drivers.

Wetland bacterial communities are highly sensitive to altered hydrology and the associated change in water physicochemical and biological properties leading to shifts in community composition and diversity, hence affecting the ecological roles. However, relevant studies are lacking in the wetlands of central Himalayas Nepal. Thus, we aimed to explore the variation of bacterial communities, diversity, and ecologic functions in the wet and dry periods of a wetland (designed as Ramsar site, Ramsar no 2257) by using 16S rRNA gene-based Illumina MiSeq sequencing. We reported a pronounced variation in water physicochemical and biological properties (temperature, pH, Chla, DOC, and TN), bacterial diversity, and community composition. Bacterial communities in the dry season harbored significantly higher alpha diversity, while significantly higher richness and abundance were reflected in the wet season. Our results uncovered the effect of nutrients on bacterial abundance, richness, and community composition. Fourteen percent of the total OTUs were shared in two hydrological periods, and the largest portion of unique OTUs (58%) was observed in the dry season. Planctomycetes and Bacteroidetes dominated the wet season exclusive OTUs; meanwhile, Actinobacteria dominated the dry season exclusive OTUs. Bacteria in these wetlands exhibited divergent ecological functions during the dry and wet seasons. By disclosing the variation of water bacterial communities in different hydrologic periods and their relationship with environmental factors, this first-hand work in the Ramsar site of Nepal will develop a baseline dataset for the scientific community that will assist in understanding the wetland's microbial ecology and biogeography.

Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

Spatial variation of bacterial community composition at the expiry of spring phytoplankton bloom in Sendai Bay, Japan

Bacterial communities inhabiting alpine lakes are essential to our understanding of ecosystem processes in a changing climate, but little has been reported about the vertical patterns of sediment bacterial communities in alpine lakes. To address this knowledge gap, we collected the 100 cm long sediment core from the center of Lake Sayram, the largest alpine lake in Xinjiang Uygur autonomous area, China, and used 16S rRNA gene-targeted amplicon sequencing to examine the bacterial populations. The results showed that bacterial diversity, as estimated by the Shannon index, was highest at the surface (6.9849 at 0–4 cm) and gradually decreased with depth up to 3.9983 at 68–72 cm, and then increased to 5.0927 at 96–100 cm. A total of 56 different phyla and 1204 distinct genera were observed in the sediment core of Lake Sayram. The bacterial community structure in the sediment samples from the various layers was dissimilar. The most abundant phyla in alpine Lake Sayram were Proteobacteria, Firmicutes, and Planctomycetes, accounting for 73%, 6%, and 4% of the total reads, respectively; the most abundant genera were Acinetobacter, Hydrogenophaga, and Pseudomonas, accounting for 18%, 12%, and 8% of the total reads, respectively. Furthermore, the relative abundance of Acinetobacter increased with sediment depth, while the relative abundance of Hydrogenophaga and Pseudomonas decreased with sediment depth. Our findings indicated that the nitrate-reducing bacteria (Acinetobacter, Hydrogenophaga, and Pseudomonas) may be prevalent in the sediment core of Lake Sayram. Canonical correspondence analysis showed that carbonate and total organic carbon (TOC) may be the main environmental factors affecting the vertical patterns of bacterial community composition (BCC) in the sediment of Lake Sayram. This work significantly contributes to our understanding of the BCC of sediments from alpine lakes in arid and semiarid regions.

The process of interaction between the plant and soil microbial communities holds the key to understanding the biogeochemical cycle and preserving the stability of vegetation ecosystems. Owing to this significance, the primary goal of this research was to give a starting point and reference methods to restore local vegetation. The vegetation distribution in the mountainous area of the upper reaches of the Heihe River Basin had notable vertical zonality, which was characterized by five typical vegetation types, including cushion vegetation(CV), herbage meadow(HM), forest steppe(FS), mountainous steppe(MS), and desert grassland(DG). The organization and diversity of soil bacterial communities in various vegetation types were examined using high-throughput sequencing techniques in both the winter and summer seasons. Sampling sites were chosen in each of the five common vegetation types in turn. Additionally, based on the FAPROTAX database, the predicted functions of microbial communities were evaluated for different vegetation types and seasons. The redundancy analysis and structural equation model were also used to investigate the primary environmental elements and uncover the mechanisms affecting the soil bacterial populations. The findings revealed that:① the physical and chemical properties of soil differed significantly among vegetation types and seasons, and the property indices varied dissimilarly with depth. In particular, the soil water content(SWC) and nutrient content of total organic carbon(TOC) and total nitrogen(TN) were significantly higher in forest grassland(FS). ② The divergences of α-diversity indices among seasons(P<0.05) were greater than that of vegetation types(P>0.05). The Chao1 index measuring the abundance of the bacterial community was higher in winter. According to the Shannon index, the species of the bacterial community were dispersed in a "W" shape in the summer and a "hump" form in the winter with altitude. ③ The predominant phyla of the bacterial community, composed of Acidobacteria, Proteobacteria, and Actinobacteria, did not significantly differ from one another. However, the organization of the bacterial community presented a significant variation seasonally at the genus level. ④ The primary functions of the soil bacterial population, which largely consisted of chemoheterotrophy, nitrification, and aerobic ammonia oxidation, were not significantly different among vegetation types and seasons. ⑤ The key factors affecting soil bacterial communities at the genus level varied significantly among seasons, with soil temperature(ST), total organic carbon(TOC), and pH in winter and soil water content(SWC), carbon-nitrogen ratio(C/N), and pH in summer. ⑥ Synergized by interrelated environmental factors, soil physical and chemical features exerted a more direct impact on the diversity and functionality of bacterial communities compared with vegetation types, including significantly changing the abundance of Acidobacteria and Bacteroidetes, as well as the role of nitrification and ammonia oxidation. Hence, improving the carbon and nitrogen contents in soil nutrients would help to enhance the diversity and function of bacterial communities. The findings of this study provided a model for determining the mechanism of regional vegetation degradation and preserving the stability of alpine ecosystems in this area by revealing the seasonal distribution pattern of bacterial communities and the key biological processes beneath the typical vertical vegetation band in the upper reaches of the Heihe River.

Bacterial community composition and function shift with the aggravation of water quality in a heavily polluted river

Clarifying the bacterial community composition and function in alkali soils is pivotal to the soil capability of sustaining venerable ecosystems. Using MiSeq sequencing, PICRUSt, and Biolog ( https://www.biolog.com ), we investigated the bacterial community composition and metabolic function of microbes in three soils differing in the severity of alkalinity. A high level of alkalinity deceased the diversity of microbial community and altered microbial community composition with the increase in relative abundances of 21 genera. The linear discriminate analysis and effect size analysis found most of 54 biomarkers belonged to Actinobacteria and Proteobacteria. Redundancy analysis indicated that the succession of bacterial community and metabolic characteristics of microbes were highly affected by the nutrient availability and soil moisture. The utilization rates of carbohydrates, amino acids, carboxylic acids, polymers, phenolic compound, and aminesides by microbes were positively correlated with soil nutrient concentrations but negatively correlated with the exchangeable sodium percentage and pH. Severe alkalinity inhibited the microbial community diversity and function on carbohydrate metabolisms.