Distribution of bacterial communities across plateau freshwater lake and upslope soils

Non-pathogenic microbiome associated to aquatic plants and anthropogenic impacts on this interaction

The microbiota associated with aquatic plants plays a crucial role in promoting plant growth and development. The structure of the plant microbiome is shaped by intricate interactions among hosts, microbes, and environmental factors. Consequently, anthropogenic pressures that disrupt these interactions can indirectly impact the ecosystem services provided by aquatic plants, such as CO2 fixation, provision of food resources, shelter to animals, nutrient cycling, and water purification. Presently, studies on plant-microbiota interactions primarily focus on terrestrial hosts and overlook aquatic environments with their unique microbiomes. Therefore, there is a pressing need for a comprehensive understanding of plant microbiomes in aquatic ecosystems. This review delves into the overall composition of the microbiota associated with aquatic plant, with a particular emphasis on bacterial communities, which have been more extensively studied. Subsequently, the functions provided by the microbiota to their aquatic plants hosts are explored, including the acquisition and mobilization of nutrients, production of auxin and related compounds, enhancement of photosynthesis, and protection against biotic and abiotic stresses. Additionally, the influence of anthropogenic stressors, such as climate change and aquatic contamination, on the interaction between microbiota and aquatic plants is discussed. Finally, knowledge gaps are highlighted and future directions in this field are suggested.

Metagenomic analysis of soil microbial communities associated with Poa alpigena Lindm in Haixin Mountain, Qinghai Lake

To investigate the impact of Poa alpigena Lindm on rhizosphere and bulk soil microorganisms in Haixin Mountain, Qinghai Lake, this study employed metagenomics technology to analyze the microbial communities of the samples. Results showed that 65 phyla, 139 classes, 278 orders, 596 families, 2376 genera, and 5545 species of soil microorganisms were identified from rhizosphere and bulk soil samples. Additionally, a microbial gene library specific to Poa alpigena Lindm was established for Qinghai Lake. Through α-diversity analysis, the richness and diversity of bulk microorganisms both significantly had a higher value than that in rhizosphere soil. The indicator microorganisms of rhizosphere and bulk soil at class level were Actinobacteria and Alphaproteobacteria, respectively. KEGG pathway analysis indicated that Carotenoid biosynthesis, Starch and sucrose metabolism, Bacterial chemotaxis, MAPK signaling pathway, Terpenoid backbone biosynthesis, and vancomycin resistance were the key differential metabolic pathways of rhizosphere soil microorganisms; in contrast, in bulk soil, the key differential metabolic were Benzoate degradation, Glycolysis gluconeogenesis, Aminobenzoate degradation, ABC transporters, Glyoxylate and dicarboxylate metabolism, oxidative phosphorylation, Degradation of aromatic compounds, Methane metabolism, Pyruvate metabolism and Microbial metabolism diverse environments. Our results indicated that Poa alpigena Lindm rhizosphere soil possessed selectivity for microorganisms in Qinghai Lake Haixin Mountain, and the rhizosphere soil also provided a suitable survival environment for microorganisms.

Soil bacterial community composition in rice-turtle coculture systems with different planting years

The rice-turtle coculture system is the most special rice-fish integrated farming system. In this study, we selected four paddy fields, including a rice monoculture paddy and three rice-turtle paddies with different planting years, to investigate the soil bacterial community composition with Illumina MiSeq sequencing technology. The results indicated that the contents of soil available nitrogen (AN), soil available phosphorus (AP) and soil organic matter (OM) in 9th year of rice-turtle paddy (RT9) were increased by 5.40%, 51.11% and 23.33% compared with rice monoculture paddy (CK), respectively. Significant differences of Acidobacteria, Desulfobacteria, Crenarchaeota were observed among the different rice farming systems. The relative abundance of Methylomonadaceae, Methylococcaceae and Methylophilaceae in RT9 was significantly higher than that in other treatments. RT9 had significantly lower relative abundance of Acidobacteria, but significantly higher relative abundance of Proteobacteria than other treatments. Redundancy analysis showed that soil AN and AP contents were the major factors influencing the abundance of the dominant microbes, wherein Methylomonadaceae, Methylococcaceae and Methylophilaceae were positively correlated with OM. The findings revealed the rice-turtle coculture system in the 9th year had higher soil nutrients and soil bacterial diversity, but there was also a risk of increasing methane emissions.

Effect of metal pollution on the distribution and co-occurrence pattern of bacterial, archaeal and fungal communities throughout the soil profiles

Metal pollution has raised negative impact on microbes, but little is known about the distribution and co-occurrence pattern of bacterial, fungal and archaeal communities along the soil profiles at multiple metal contamination sites. Here, we characterized the variations of metal concentrations and microbial communities with soil depth along five deep bores at the Tanghe Sewage Reservoir, a typical metal contamination area on the North China Plain. Co, Cd, Mg, Se, and Li were identified as the major contaminants in this area, and the pollution load index was 1.88, 1.54 and 1.62 in the shallow layer (0-0.6 m), deep layer (>2.0 m) and middle layer (0.6-2.0 m), respectively. The diversities and compositions of bacterial, archaeal and fungal communities varied significantly along the soil profiles. Deterministic process played a crucial role in shaping the difference of microbial community compositions among different soil layers, in which metal levels contributed more than soil physiochemical parameters. Furthermore, the interspecific co-occurrence network was most complex in the middle layer, indicating that metal pollution could decrease microbial network complexity. Bacterial keystone species in the co-occurrence networks showed both positive and negative correlations with polluted metals, whereas most archaeal and fungal keystone species were negatively related to multiple metals. These findings increased our understanding of distribution patterns, co-occurrence networks and environmental drivers of microbial communities in metal pollution soils.

Effects of environmental factors on the distribution of microbial communities across soils and lake sediments in the Hoh Xil Nature Reserve of the Qinghai-Tibetan Plateau

Comparison of microbial community diversity and composition of terrestrial and aquatic ecosystems in undisturbed regions could expand our understanding on the mechanisms of microbial community assembly and ecosystem responses to environmental change. This study investigated the spatial distribution of bacterial community diversity and composition in the lakeshore soils and lake sediments from one of the best preserved nature reserves, Hoh Xil on the Qinghai-Tibetan Plateau, and explored the corresponding environmental drivers. A total of 36 sediment and soil samples were collected from six alpine lakes and the corresponding shore zones, and their bacterial community structure was identified by high-throughput 16S rRNA gene sequencing. Significant difference (p < 0.05) in diversity and composition of bacterial communities between the soils and sediments was observed. Heterogeneous selection played a dominant role in shaping the spatial variations of bacterial communities between the soils and sediments. Results of canonical correspondence analysis showed that the difference in composition of bacterial communities at OTU level between the soils and sediments was mainly determined by the mean annual temperature, salinity, and contents of total organic carbon and total nitrogen. Structural equation modeling revealed that salinity played a significantly direct role in soil bacterial composition, while mean annual temperature indirectly affected the bacterial composition mainly through changing soil salinity. In contrast, the sediment bacterial composition was directly influenced primarily by the contents of total organic carbon and total nitrogen, while pH also had an important indirect effect on sediment bacterial composition. These results shed light on the distribution patterns of bacterial communities between lakeshore soils and lake sediments in high-altitude permafrost regions, and the major ecological processes and environmental drivers that shaped their bacterial communities, and provide insight into the mechanisms underlying microbial community assembly in such regions.

Insight into functional microorganisms in wet–dry conversion to alleviate the toxicity of chromium fractions in red soil

Soil contamination with potentially toxic element such as chromium (Cr) poses a threat to the environment and human health. The environmental toxicity of Cr is related not only to the total Cr content but also to the distribution of Cr fractions. In this study, laboratory simulation experiments were conducted to explore the characteristics of Cr fractions and responses of the functional microbial community during dynamic leaching and static drying processes. The results showed that acid-soluble Cr and reducible Cr transformed into other relatively stable fractions under dry conditions, and ammonium nitrogen promoted the transformation. Nitrate-nitrogen was significantly positively correlated with Cr fractions in the wet stage (p < 0.05), while ammonium nitrogen showed the same relation in the dry process. Analysis of the microbial community showed that the bacterial and fungal genera Flavihumibacter, Altererythrobacter, Methylobacillus, Flavisolibacter, Lysobacter, and Cladosporium were related to the Cr fractions (acid-soluble Cr, reducible Cr, and oxidizable Cr) under wet conditions, while the microbial genera Ellin6067, MND1, and Ramlibacter were related to Cr fractions under dry conditions. Moreover, the proliferation of the functional microbial genera Methylobacillus, Ellin6067, and MND1 related to Cr fractions in the wet–dry conversion process alleviated the environmental toxicity of Cr. These findings provide useful information for the remediation of Cr-contaminated soils by monitoring the distribution fractions of Cr and the functional microbial community under wet–dry conditions.

Effects of sediment physicochemical factors and heavy metals on the diversity, structure, and functions of bacterial and fungal communities from a eutrophic river

Urbanization has destroyed river ecosystems, leading to eutrophication. Heavy metals are frequently observed in urban rivers, and the joint effects of eutrophication and heavy metals on microbial communities, especially on fungal communities, have not been adequately explored. In this study, we explored the effect of sediment physicochemical factors and heavy metals on the microbial diversity, community structure, and functions of bacterial and fungal communities from a black-odorous river in Wuhu, China. Twenty-four samples were collected, and the diversity and structure of fungal and bacterial communities were determined by high-throughput sequencing. Proteobacteria and Rozellomycota were the main phyla in the bacterial and fungal communities, respectively. The results showed different distribution patterns of bacterial and fungal communities along the river. Physicochemical factors and heavy metals exhibited different effects on microbial variation. Specifically, pH and Cr negatively affected bacterial α-diversity, whereas total phosphorus and Cr significantly affected fungal α-diversity. Variance partitioning analysis revealed that physicochemical factors explained more of the bacterial community structure than heavy metals (49.5% vs. 36.6%), with pH and total phosphorus being the dominant factors. Opposite patterns were observed for fungal community structure, with heavy metals contributing the most (48.0%). A similar influence pattern was observed for the predicted functions of the two communities. This study suggests that heavy metals in eutrophication rivers are essential factors that shift the microbial variation and should be considered in urban river evaluation and remediation.

Comparative characterization of microbial communities that inhabit PFAS-rich contaminated sites: A case-control study

The historic usage and discharge of per- and polyfluoroalkyl substances (PFAS) containing chemicals have produced many contaminated sites and PFAS contamination has become a global concern due to their persistence, widespread distribution, and potential adverse impacts for human and environmental health. However, there have been limited investigations on the specific behavior of bacterial communities in PFAS contaminated soils. In this study, a quantitative PCR assay and Illumina MiSeq sequencing were used to investigate the variations of bacterial communities in a regional Australian airport contaminated with PFAS. The dominate PFAS detected in soil samples was Perfluorooctanesulfonic acid (PFOS), which accounted for 82% of total PFAS and the maximum PFOS level was noted (20,947±1824 ng.PFOS/mg.Soil) at the top soil. Irrespective of the degree of PFAS contamination at different depths, the comparable percentile contribution of each PFAS was observed in soil samples. Significantly higher bacteria amplicon sequence variant (ASV) and diversity were noted in uncontaminated soil than PFAS contaminated soil. Bacterial genera Rhodanobacter and Chujaibacter were dominant in the PFAS contaminated soil. Three different bacterial genera of Alphaproteobacteria, Ambiguous taxa of Acidobacteriia, and genus Chujaibacter of Gammaproteobacteria showed a significant positive correlation and RB41, Gaiella showed a significant negative correlation with 11 different PFAS concentrations. Overall, the results presented in this study suggest that the counts and species diversity of soil microorganisms are adversely influenced by PFAS contamination.

Insights into the vertical distribution of the microbiota in steel plant soils with potentially toxic elements and PAHs contamination after 60 years operation: Abundance, structure, co-occurrence network and functionality

Both potentially toxic elements (PTEs) and polycyclic aromatic hydrocarbons (PAHs) are widely present in soil contaminated by steel industries. This study assessed the vertical variation (at 20 cm, 40 cm, 60 cm, 80 cm, 120 cm, and 150 cm depth) of bacterial abundance, community structure, functional genes related to PAHs degradation, and community co-occurrence patterns in an old steel plant soils which contaminated by PTEs and PAHs for 60 years. The excessive PAHs and PTEs in steel plant soils were benzo (a) pyrene, benzo (b) fluoranthene, dibenzo (a, h) anthracene, indeno (1,2,3-c, d) pyrene, and lead (Pb). The abundance and composition of bacterial community considerably changed with soil depth in two study areas with different pollution degrees. The results of co-occurrence network analysis indicated that the top genera in blast furnace zone identified as the potential keystone taxa were Haliangium, Blastococcus, Nitrospira, and Sulfurifustis. And in coking zone, the top genera were Gaiella. The predictions of bacterial metabolism function using PICRUSt showed that the PAHs-PTEs contaminated soil still had the potential for PAHs degradation, but most PTEs negatively correlated with PAHs degradation genes. The total sulfur (TS), acenaphthene (ANA), and Zinc (Zn) were the key factors to drive development of bacterial communities in the steel plant soils. As far as we know, this is the first investigation of vertical distribution and interaction of the bacterial microbiota in the aging soils of steel plant contaminated with PTEs and PAHs.

Soil bacterial community composition in rice-fish integrated farming systems with different planting years

The high productivity and efficient nutrient utilization in rice–fish integrated farming system are well reported. However, the characteristics of soil bacterial communities and their relationship with soil nutrient availability in rice–fish field remain unclear. In this study, we selected three paddy fields, including a rice monoculture field and two rice–fish fields with different planting years, to investigate the soil bacterial community composition with Illumina MiSeq sequencing technology. The results indicated that the soil properties were significantly different among different rice farming systems. The soil bacterial community composition in the rice–fish field was significantly different from that in the rice monoculture field. Five of the top 15 phyla were observed with significant differences and Nitrospirae was the most significant one. However, no taxa observed with significance between the rice planting area and aquaculture area no matter in the 1st or 5th year of rice–fish field. RDA analysis showed that the soil bacterial community differentiation in the 5th year of rice–fish field was positively correlated with soil properties, such as AN and OM contents, EC and pH value. Although the rice yields in rice–fish field decreased, the net economic benefit of the rice–fish system enhanced obviously due to the high value of aquaculture animals.

Metagenome sequencing to unveil the resistome in a deep subtropical lake on the Yunnan-Guizhou Plateau, China

Erhai Lake in the Yunnan-Guizhou Plateau, a typical subtropical deep lake, experienced long-time input of nutrients and pollutants, which provides beneficial conditions for evolution and spread of resistance genes. In this study, the profile of bacterial community, antibiotic and metal resistance genes in sediments of Erhai Lake were analyzed via high-thought sequencing of 16S rRNA and metagenomic DNA. Proteobacteria, Firmicutes, Nitrospirae, and Bacteroidetes were found to be the main composition of the bacterial community. Multidrug-, bacitracin-, macrolide-lincosamide-streptogramin (MLS)- and tetracycline resistance genes were the primary antibiotic resistance gene (ARG) types with high relative abundance, whereas Multi-metal-, and arsenic- resistance genes were the primary metal resistance gene (MRG) types. The effects of nitrogen and phosphorus on the abundance of ARGs and MRGs depended on the different types. Some specific ARG (fosmidomycin resistance genes) and MRG types (multi-metal resistance genes) also showed significant geographic distribution. Bacterial community was the main driver shaping the resistome. Nutrients also played an essential role in structuring the bacterial community and resistome in the sediments of Erhai Lake. This study sheds light on the distribution and fate of resistome under a high load of nitrogen and phosphorus in a deep lake.

Assessing Chromium Contamination in Red Soil: Monitoring the Migration of Fractions and the Change of Related Microorganisms

The improper stacking of chromium (Cr) slag poses a great threat to the environment and human health. The toxicity of Cr in soil is not only related to its total amount, but also to its fractions. A simulated experiment was conducted in laboratory to assess the environmental risk of Cr fractions migration and distribution in red soil. The results showed the content of acid-soluble and reducible Cr significantly decreased (P < 0.05) in top layer but increased in middle and substratum layers over time. This indicated that acid-soluble and reducible Cr migrated downward with time and the relative mobility of acid-soluble Cr (0.038 mg/kg·d·m) was higher than that of reducible Cr (0.028 mg/kg·d·m). Furthermore, correlation analysis between microbial community and chromium fraction showed the relative abundance of Lysobacter, Flavihumibacter, Flavisolbacter, and Altererythrobacter was significantly (P < 0.05) correlated with acid-soluble and reducible fractions. Thus, these microorganisms might be evaluators to assess the migration of acid-soluble and reducible fractions in red soil. In summary, this study provided a new comprehension on remediation of Cr-contaminated soil by monitoring the migration of acid-soluble and reducible fractions and the changes of related microbial groups.

Phytoplankton and Bacterial Community Structure in Two Chinese Lakes of Different Trophic Status

Phytoplankton are the primary producers at the basis of aquatic food webs, and bacteria play an important role in energy flow and biochemical cycling in aquatic ecosystems. In this study, both the bacterial and phytoplankton communities were examined in the oligotrophic Lake Basomtso and the eutrophic Lake South (China). The results of this study showed that the phytoplankton density and diversity in the eutrophic lake were higher than those in the oligotrophic lake. Furthermore, Chlorophyta (68%) and Cryptophyta (24%) were the dominant groups in the eutrophic lake, while Bacillariophyta (95%) dominated in the oligotrophic lake. The bacterial communities in the waters and sediments of the two lakes were mainly composed of Proteobacteria (mean of 32%), Actinobacteria (mean of 25%), Bacteroidetes (mean of 12%), and Chloroflexi (mean of 6%). Comparative analysis showed that the abundance of bacteria in the eutrophic lake was higher than that in the oligotrophic lake (p < 0.05), but the bacterial diversity in the oligotrophic lake was higher than that in the eutrophic lake (p < 0.05). Finally, the bacterial abundance and diversity in the sediments of the two lakes were higher than those in the water samples (p < 0.05), and the Latescibacteria and Nitrospinae groups were identified only in the sediments. These results suggest that both the phytoplankton and bacterial communities differed considerably between the oligotrophic lake and the eutrophic lake.

Evaluation of the Human Interference on the Microbial Diversity of Poyang Lake Using High-Throughput Sequencing Analyses

The Poyang Lake Watershed (PLW) is regarded as an air temperature moderator, as well as a wind energy, food resources and good habitat in the Jiangxi Province, People’s Republic of China. However, with the increasing of anthropogenic disturbance on PLW, there are few studies focused on the effects of human activities on microbial composition in Poyang Lake. In the present study, a high-throughput sequencing method was used to identify the microbial composition in water and sludge in Dahuchi (DHC, sub-lake of Poyang Lake National Nature Reserve), Shahu (SH, sub-lake of Poyang Lake National Nature Reserve), Nanhu (NH, sub-lake out of Poyang Lake National Nature Reserve), Zhelinhu (ZLH, artificial reservoir), Sixiahu (SXH, sub-lake artificially isolated from Poyang Lake) and Qianhu (QH, urban lake). Results of the present study illustrated the various bacterial diversity between different lakes, for example, at the phylum level, Actinobacteria and Cyanobacteria showed low abundance in water samples of ZLH and QH, and high abundance in DHC. In addition, anthropogenic disturbance and human activities decreased the abundance of probiotic bacteria (Actinobacteria, Cyanobacteria, Chloroflexi and Acidobacteria) and increased the abundance of pathogenic bacteria (Acinetobacter, Aeromonas and Noviherbaspirillum). The enrichment of pathogenic bacteria in polluted lakes, in turn, may cause potential threats to human health.

Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community

Methanogenesis occurs in many natural environments and is used in biotechnology for biogas production. The efficiency of methane production depends on the microbiome structure that determines interspecies electron transfer. In this research, the microbial community retrieved from mining subsidence reservoir sediment was used to establish enrichment cultures on media containing different carbon sources (tryptone, yeast extract, acetate, CO₂/H₂). The microbiome composition and methane production rate of the cultures were screened as a function of the substrate and transition stage. The relationships between the microorganisms involved in methane formation were the major focus of this study. Methanogenic consortia were identified by next generation sequencing (NGS) and functional genes connected with organic matter transformation were predicted using the PICRUSt approach and annotated in the KEGG. The methane production rate (exceeding 12.8 mg CH₄ L⁻¹ d⁻¹) was highest in the culture grown with tryptone, yeast extract, and CO₂/H_2. The analysis of communities that developed on various carbon sources casts new light on the ecophysiology of the recently described bacterial phylum Caldiserica and methanogenic Archaea representing the genera Methanomassiliicoccus and Methanothrix. Furthermore, it is hypothesized that representatives of Caldiserica may support hydrogenotrophic methanogenesis.

Bacterial and archaeal spatial distribution and its environmental drivers in an extremely haloalkaline soil at the landscape scale

Background

A great number of studies have shown that the distribution of microorganisms in the soil is not random, but that their abundance changes along environmental gradients (spatial patterns). The present study examined the spatial variability of the physicochemical characteristics of an extreme alkaline saline soil and how they controlled the archaeal and bacterial communities so as to determine the main spatial community drivers.

Methods

The archaeal and bacterial community structure, and soil characteristics were determined at 13 points along a 211 m transect in the former lake Texcoco. Geostatistical techniques were used to describe spatial patterns of the microbial community and soil characteristics and determine soil properties that defined the prokaryotic community structure.

Results

A high variability in electrolytic conductivity (EC) and water content (WC) was found. Euryarchaeota dominated Archaea, except when the EC was low. Proteobacteria, Bacteroidetes and Actinobacteria were the dominant bacterial phyla independent of large variations in certain soil characteristics. Multivariate analysis showed that soil WC affected the archaeal community structure and a geostatistical analysis found that variation in the relative abundance of Euryarchaeota was controlled by EC. The bacterial alpha diversity was less controlled by soil characteristics at the scale of this study than the archaeal alpha diversity.

Discussion

Results indicated that WC and EC played a major role in driving the microbial communities distribution and scale and sampling strategies were important to define spatial patterns.

Dynamics of bacterial community in Tonle Sap Lake, a large tropical flood-pulse system in Southeast Asia

Tonle Sap Lake, the largest freshwater body in Southeast Asia, plays an important role in lives and environment. The lake is reportedly under anthropogenic pressure and suffers from eutrophication. The floating villagers suffer from waterborne diseases. However, the shift in bacterial community due to human activities in this great lake has not yet been reported. We aimed to determine the dynamics of the bacterial community and their concentration in the lake using 67 surface waters, 53 sub-layer waters and 59 sediment samples by Next Generation Sequencing (NGS). The bacterial communities in the surface water and sub-layer water were similar but they differed from the sediment; however, their abundance showed spatiotemporal variations. The bacterial diversity reached the highest value in the dry season but lowest value in the rainy season in the surface water and sediment. Their diversity in the sub-layer water was highest in the transition from dry to rainy season. The total 16S rRNA gene copy number in the sediment were >100 times higher than that measured in the water. The Cyanobacteria, Actinobacteria, and Proteobacteria concentrations in the lake water increased in the dry season and reached a peak in the transition from dry to rainy season. The concentrations of Proteobacteria and Firmicutes elevated in the lake water and sediment, respectively, in the floating villages which were >10 times higher than the places with non-point sources. The bacterial concentration and its diversity in the Tonle Sap Lake changed based on the lake water volume between rainy and dry season. The bacterial concentration in the Tonle Sap Lake diluted with the water inflow from Mekong River and its tributaries in the rainy season. As influenced by the fecal waste, the bacterial community in the floating villages differed from the places with non-point source.

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

Vertical distribution of microbial communities in soils contaminated by chromium and perfluoroalkyl substances

Both Bacteria and Archaea are important players in soil biogeochemical cycles. Both chromium (Cr) and perfluoroalkyl substances (PFASs) are widely present in soil environment. However, the depth-related distribution of microbial community in soils contaminated by Cr or/and PFASs remains unknown. Hence, the present study applied quantitative PCR assay and Illumina MiSeq sequencing to investigate the vertical variations of archaeal and bacterial communities in soils (0.5-12.5m depth) contaminated by chrome plating waste and the potential effects of Cr and PFASs. Both bacterial and archaeal communities displayed the remarkable depth-related changes of abundance (2.16×10⁷-5.05×10⁹ and 4.95×10⁵-2.56×10⁸ 16S rRNA gene copies per gram dry soil respectively for Bacteria and Archaea), diversity (bacterial and archaeal Shannon diversity indices of 5.06-6.34 and 2.91-4.61, respectively) and structure. However, at each soil depth, bacterial community had higher abundance, richness and diversity than archaeal community. Soil bacterial communities were mainly composed of Proteobacteria, Chloroflexi, Actinobacteria and Firmicutes, and archaeal communities were dominated by Thaumarchaeota and unclassified Archaea. Moreover, microbial abundance and richness increased with increasing perfluorohexane sulfonate (PFHxS) content. Microbial abundance was correlated to total Cr, and archaeal richness was correlated to total Cr and Cr(IV). In addition, total Cr might be a key determinant of soil microbial community structure.

Bacterial community analysis of anoxic/aeration (A/O) system in a combined process for gibberellin wastewater treatment

Gibberellin wastewater cannot be directly discharged without treatment due to its high concentrations of sulfate and organic compounds and strong acidity. Therefore, multi-stage anaerobic bioreactor + micro-aerobic+ anoxic/aeration (A/O) + biological contact oxidation combined processes are used to treat gibberellin wastewater. However, knowledge of the treatment effects of the A/O process and bacterial community structure in the aeration tank reactors of such systems is sparse. Therefore, this study was conducted to investigate the treatment effects and operation of the A/O process on gibberellin wastewater, as well as changes in the bacterial community structure of activated sludge in the aeration tank during treatment. Moreover, removal was examined based on evaluation of effluent after A/O treatment. Although influent chemical oxygen demand (COD), NH₃-N and total phosphorus (TP) fluctuated, effluent COD, NH₃-N and TP remained stable. Moreover, average COD, NH₃-N and TP removal efficiency were 68.41%, 93.67% and 45.82%, respectively, during the A/O process. At the phylum level, Proteobacteria was the dominant phylum in all samples, followed by Chloroflexi, Bacteroidetes and Actinobacteria. Proteobacteria played an important role in the removal of organic matter. Chloroflexi was found to be responsible for the degradation of carbohydrates and Bacteroidetes also had been found to be responsible for the degradation of complex organic matters. Actinobacteria are able to degrade a variety of environmental chemicals. Additionally, Anaerolineaceae_uncultured was the major genus in samples collected on May 25, 2015, while Novosphingobium and Nitrospira were dominant in most samples. Nitrosomonas are regarded as the dominant ammonia-oxidizing bacteria, while Nitrospira are the main nitrite-oxidizing bacteria. Bacterial community structure varied considerably with time, and a partial Mantel test showed a highly significant positive correlation between bacterial community structure and DO. The bacterial community structure was also positively correlated with temperature and SO₄^2-.

Microbial diversity on commercial eggs as affected by the production system. A first approach using PGM

A novel DNA-based technique (PGM) has been employed for first time to analyse commercial eggs with the advantage of allowing an exhaustive identification of the microbiota present. Eggs from two different production systems, i.e. a free range system and a cage system, were analysed. Twenty-one and twenty-two phyla were identified on the surface of cage system and free range system eggs, respectively. In both cases, Firmicutes was the dominant phylum (representing around 50% of total phyla), being found families frequently reported to be present in the intestinal microbiota of chickens or hens, such as Clostridiaceae, Ruminococcaceae and Lachnospiraceae. Additionally, other phyla and families not previously described in association with eggshells could also be identified in this work. Most of the potential pathogenic genera associated with eggs (Salmonella, Clostridium, Helicobacter, Pseudomonas and Staphylococcus) showed higher incidence in eggs coming from cage systems than in eggs coming from free range systems, although the abundance of these genera were very low in both cases (<5% of total bacteria).

Bacterial community diversity on in-shell walnut surfaces from six representative provinces in China

Walnuts (Juglans regia) have been associated with foodborne illness outbreaks in recent years. Thus, the purpose of this study was to investigate the distribution of bacteria on in-shell walnut surfaces from six representative provinces in China. The bacterial populations on walnut surfaces were investigated by high-throughput sequencing based on the bacterial 16 S rRNA hypervariable region V4. Twenty-eight samples were collected from fourteen regions in six provinces and harvested in different periods (the fresh in 2016 and the old in 2015). Proteobacteria was the most dominant phylum in all samples except for XJ1. In XJ1, and the most abundant phylum was Cyanobacteria, which also accounted for a large proportion of the abundance in YN1, YN11, XJ2 and SC11. In addition, Firmicutes and Actinobacteria were also the abundant phyla in the given samples. Some genera belonging to the opportunistic pathogens were detected, such as Pseudomonas, Acinetobacter, Burkholderia and Bacillus. The results revealed that the composition and abundance of bacterial consortiums on walnut surfaces varied among the geographical sites where they were harvested. Moreover, the storage time of samples also had impact on the abundance of bacteria. This study may provide a better understanding of the bacterial communities' diversity on in-shell walnut surfaces.