Structure and succession dynamics of a Neotropical freshwater periphyton community, with emphasis on ciliates and their association with bacterial taxa

Periphyton communities in freshwater systems play an essential role in biogeochemical processes, but knowledge of their structure and dynamics lags far behind other environments. We used eDNA metabarcoding of 16S and 18S rRNA markers to investigate the formation and establishment of a periphytic community, in addition to morphology-based analyses of its most abundant group (peritrich ciliates). We sampled two nearby sites within a large Neotropical lake at four time points, aiming to assess whether periphyton establishment can be replicated on this local scale. Producers and denitrifiers were abundant in the community, illustrating the relevant role of biofilms in freshwater nutrient recycling. Among microeukaryotes, peritrich ciliates dominated the community, with genera Epistylis and Vorticella being the most abundant and showing a clear succession at both sites. Other ciliates were identified and, in some cases, their occurrence was strongly related to bacterial abundance. The structure and succession dynamics of both prokaryotic and eukaryotic components of periphyton differed between the two sites, in spite of their adjacent locations and similar abiotic properties, indicating that the establishment of these communities can vary even on a local scale within a lake ecosystem.

Heterotrophic Bacterioplankton Growth and Physiological Properties in Red Sea Tropical Shallow Ecosystems With Different Dissolved Organic Matter Sources

Despite the key role of heterotrophic bacterioplankton in the biogeochemistry of tropical coastal waters, their dynamics have been poorly investigated in relation to the different dissolved organic matter (DOM) pools usually available. In this study we conducted four seasonal incubations of unfiltered and predator-free seawater (Community and Filtered treatment, respectively) at three Red Sea coastal sites characterized by different dominant DOM sources: Seagrass, Mangrove, and Phytoplankton. Bacterial abundance, growth and physiological status were assessed by flow cytometry and community composition by 16S rRNA gene amplicons. The Seagrass site showed the highest initial abundances (6.93 ± 0.30 × 105 cells mL–1), coincident with maximum DOC concentrations (>100 μmol C L–1), while growth rates peaked at the Mangrove site (1.11 ± 0.09 d–1) and were consistently higher in the Filtered treatment. The ratio between the Filtered and Community maximum bacterial abundance (a proxy for top-down control by protistan grazers) showed minimum values at the Seagrass site (1.05 ± 0.05) and maximum at the Phytoplankton site (1.24 ± 0.30), suggesting protistan grazing was higher in open waters, especially in the first half of the year. Since the Mangrove and Seagrass sites shared a similar bacterial diversity, the unexpected lack of bacterial response to predators removal at the latter site should be explained by differences in DOM characteristics. Nitrogen-rich DOM and fluorescent protein-like components were significantly associated with enhanced specific growth rates along the inshore-offshore gradient. Our study confirms the hypotheses that top–down factors control bacterial standing stocks while specific growth rates are bottom-up controlled in representative Red Sea shallow, oligotrophic ecosystems.

Maize (Zea mays L.) Seedlings Rhizosphere Microbial Community as Responded to Acidic Biochar Amendment Under Saline Conditions

Biochar has extensively been used for multiple purposes in agriculture, including improving soil microbial biomass. The current study aimed to investigate the effect of acidic biochar on maize seedlings’ rhizosphere bacterial abundance under salinity. There were seven treatments and three replicates in a controlled greenhouse coded as B0S1, B1S1, and B2S1 and B0S2, B1S2, and B2S2. CK is control (free of biochar and salt); B0, B1, and B2 are 0, 15, and 30 g biochar (kg soil)–1; and S1 and S2 are 2.5 and 5 g salt pot–1 that were amended, respectively. After harvesting the maize seedlings, the soil samples were collected and analyzed for soil microbial biomass, bacterial abundance, and diversity. The results revealed that relative abundance of Proteobacteria, Actinobacteria, and Chloroflexi increased on phylum level, whereas Actinomarinales, Alphaproteobacteria, and Streptomyces enhanced on genus level, respectively, in B2S1 and B2S2, when compared with CK and non-biochar amended soil under saline conditions. The relative abundance of Actinomarinales was positively correlated with total potassium (TK) and Gematimonadetes negatively correlated with total phosphorus (TP). Biochar addition slightly altered the Ace1, Chao1, and alpha diversity. Principal component analysis corresponded to the changes in soil bacterial community that were closely associated with biochar when compared with CK and salt-treated soils. In conclusion, acidic biochar showed an improved soil microbial community under salinity.

Peanut/Cotton Intercropping Increases Productivity and Economic Returns by Regulating Nutrient Accumulation and Soil Microbial Communities Under both Normal and Saline Soil Conditions

Background Intercropping has been widely adopted by farmers for it often enhances crop productivity and economic returns; however, the underpinning mechanisms from the perspective of belowground interspecific interactions are only partly understood especially when intercropping under saline soil conditions. By using permeable (100 µm) and impermeable (solid) root barriers in a multi-site field experiment, we aimed to study the impact of root-root interactions on nutrient accumulation, soil microbial communities, crop yield, and economic returns in a peanut/cotton intercropping system under non-saline, secondary-saline, and coastal saline soil conditions. Results The results indicate that intercropping (IC) decreased the peanut pods yield while increased the seed cotton yield, and consequently enhanced the economic returns compared with monoculture of peanut (MP) and cotton (MC). The higher accumulations of nutrients such as nitrogen (N), phosphorus (P), and potassium (K) were also observed in IC not only in the soil but also in vegetative tissues and reproductive organs. Bacterial community structure analysis under normal growth conditions reveals that IC dramatically altered the soil bacterial abundance composition in both peanut and cotton strips of the top soil whereas the bacterial diversity was barely affected compared with MP and MC. At blossom-needling stage, the metabolic functional features of the bacterial communities such as fatty acid biosynthesis, lipoic acid metabolism, peptidoglycan biosynthesis, and biosynthesis of ansamycins were significantly enriched in MP compared with other treatments. Conversely, these metabolic functional features were dramatically depleted in MP while significantly enriched in IC at podding stage. Permeable root barrier treatments (NC-P and NC-C) counteracted the benefits of IC and the side effects were more pronounced in impermeable treatments (SC-P and SC-C). Conclusion Peanut/cotton intercropping increases crop yield as well as economic returns under non-saline, secondary-saline, and coastal saline soil conditions probably by modulating the soil bacterial abundance composition and accelerating nutrients accumulation.

Nitrogen Fertilizer Driven Bacterial Community Structure in a Semi-Arid Region of Northeast China

The soil nitrogen (N) cycle is an essential role of the biogeochemical cycle. Bacteria play an irreplaceable part in the soil N cycle, but the impact of different N gradients on bacterial communities remains unclear. The purpose of this research was to explore the bacterial abundance, community composition, and diversity under different N application rates in a water-limited area. We investigated the bacterial abundance, diversity, community composition, and structure under five different N gradients (0, 90, 150, 210, and 270 kg ha−1) using real-time quantitative PCR and high-throughput sequencing, and then explored bacterial functional groups with FAPROTAX. N application significantly affected bacterial abundance and community composition. Bacterial diversity was enhanced at low N application rates and reduced at higher N application rates. Principal coordinate analysis showed that bacterial community structure was separated into two groups between low N application rates and high N application rates; these differences in bacterial community structure may be driven by available nitrogen (AN). The results of FAPROTAX revealed that N application promoted the functions of Aerobic_nitrite_oxidation, Nitrate_reduction, and Aerobic_ammonia_oxidation, but inhibited the Nitrogen_fixation function of the bacterial community. The high N network caused the reduction of network structure stability. Our results revealed that N fertilizer driven bacterial community structure and soil nutrients were the main influential factors in the variation of bacterial community structure. We suggest that the optimal N application rate in this study may be approximately 150 kg ha−1, based on the variations of soil properties and bacterial community structure in semi-arid areas.

Effects of perfluoroalkyl and polyfluoroalkyl substances on soil structure and function

Soils are impacted at a global scale by several anthropogenic factors, including chemical pollutants. Among those, perfluoroalkyl and polyfluoroalkyl substances (PFAS) are of concern due to their high environmental persistence, and as they might affect soil health and functions. However, data on impacts of PFASs on soil structure and microbially-driven processes are currently lacking. This study explored the effects of perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA) and perfluorobutanesulfonic acid (PFBS) at environmental-relevant nominal concentrations (1 ~ 1000 ng g-1) on soil functions, using a 6-week microcosm experiment. We measured soil respiration, litter decomposition, enzyme and microbial activities, soil aggregates, and bacterial abundance. PFAS (even at 1 ng g-1 for PFBS) significantly increased the litter decomposition, associated with positive effects on bacterial abundance, and β-glucosidase activities. This effect increased with PFAS concentrations. Soil respiration was significantly inhibited by PFAS in the 3rd week, while this effect was more variable in week 6. Water-stable aggregates were negatively affected by PFOS and PFOA, possibly related to microbial shifts. The general microbial activities and β-D-cellobiosidase and phosphatase activities were barely affected by PFAS treatments. Our work highlights the potential effects of PFAS on soil health, and we argue that this substance class could be a factor of environmental change of potentially broad relevance in terrestrial ecosystem functioning.

Comammox Nitrospira bacteria outnumber canonical nitrifiers irrespective of electron donor mode and availability

Complete ammonia oxidizing bacteria coexist with canonical ammonia and nitrite oxidizing bacteria in a wide range of environments. Whether this coexistence is due to competitive or cooperative interactions between the three guilds, or a result of niche separation is not yet clear. Understanding the factors driving coexistence of nitrifying guilds is critical to effectively manage nitrification processes occurring in engineered and natural ecosystems. In this study, microcosms-based experiments were used to investigate the impact of electron donor mode (i.e., ammonia and urea) and loading on the population dynamics of nitrifying guilds in drinking water biofilter media. Shotgun sequencing of DNA from select time points followed by co-assembly and re-construction of metagenome assembled genomes (MAGs) revealed multiple clade A2 and one clade A1 comammox bacterial populations coexisted in the microcosms alongside Nitrosomonas-like ammonia oxidizers and Nitrospira-like nitrite oxidizer populations. Clade A2 comammox bacteria were likely the primary nitrifiers within the microcosms and increased in abundance over canonical ammonia and nitrite oxidizing bacteria irrespective of electron donor mode or nitrogen loading rates. This suggests that comammox bacteria will outnumber nitrifying communities sourced from oligotrophic environments irrespective of variable nitrogen regimes. Changes in comammox bacterial abundance were not correlated with either ammonia or nitrite oxidizing bacterial abundance in urea amended systems where metabolic reconstruction indicated potential cross feeding between ammonia and nitrite oxidizing bacteria. In contrast, comammox bacterial abundance demonstrated a negative correlation with that of nitrite oxidizers in ammonia amended systems. This suggests that potentially weaker synergistic relationships between ammonia and nitrite oxidizers might enable comammox bacteria to displace nitrite oxidizers from complex nitrifying communities.

Determination of bacterial abundance and communities in the nipple drinking system of cascading cage layer houses

Water quality is critical for egg production and animal health in commercial layer housing systems. To investigate microbial contamination in nipple drinking system in layer houses, the bacterial abundance and communities in water pipes and V-troughs on different tiers (e.g., 1st, 3rd, 5th, and 7th tiers) of a layer house with 8 overlapping cage tiers were determined using qRT-PCR and 16S rRNA sequencing. The water bacterial abundance (i.e., genome 16S rDNA copy number, WBCN) in water pipes and V-troughs did not significantly differ among tiers, but they were 46.77 to 1905.46 times higher in V-troughs than that in water pipes (P < 0.05) for each tier. Illumina sequencing obtained 1,746,303 effective reads from 24 water samples in V-troughs of 4 tiers (six samples from each tier). Taxonomic analysis indicated that the 1st and 5th tiers were predominated by Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, while the 3rd and 7th tiers were predominated by Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria. The top four genera were Acinetobacter, Streptococcus, Rothia and Comamonas among measured tiers. The high bacterial abundance and bacterial OTUs of water in the V-troughs reflect poor water quality, which may adversely affect growth and health of laying hens. Therefore, it is suggested that water quality in the V-tough should be checked more frequently in commercial layer houses.

Associations between Maternal Diet, Body Composition and Gut Microbial Ecology in Pregnancy

Maternal body composition, gestational weight gain (GWG) and diet quality influence offspring obesity risk. While the gut microbiome is thought to play a crucial role, it is understudied in pregnancy. Using a longitudinal pregnancy cohort, maternal anthropometrics, body composition, fecal microbiome and dietary intake were assessed at 12, 24 and 36 weeks of gestation. Fecal samples (n = 101, 98 and 107, at each trimester, respectively) were utilized for microbiome analysis via 16S rRNA amplicon sequencing. Data analysis included alpha- and beta-diversity measures and assessment of compositional changes using MaAsLin2. Correlation analyses of serum metabolic and anthropometric markers were performed against bacterial abundance and predicted functional pathways. α-diversity was unaltered by pregnancy stage or maternal obesity status. Actinobacteria, Lachnospiraceae, Akkermansia, Bifidobacterium, Streptococcus and Anaerotuncus abundances were associated with gestation stage. Maternal obesity status was associated with increased abundance of Lachnospiraceae, Bilophila, Dialister and Roseburia. Maternal BMI, fat mass, triglyceride and insulin levels were positively associated with Bilophila. Correlations of bacterial abundance with diet intake showed that Ruminococcus and Paraprevotella were associated with total fat and unsaturated fatty acid intake, while Collinsella and Anaerostipes were associated with protein intake. While causal relationships remain unclear, collectively, these findings indicate pregnancy- and maternal obesity-dependent interactions between dietary factors and the maternal gut microbiome.

Changes in soil physicochemical properties and bacterial communities at different soil depths after long-term straw mulching under a no-till system

Conservation tillage has attracted increasing attention over recent decades, mainly due to its benefits for improving soil organic matter content and reducing soil erosion. However, the effects of long-term straw mulching under a no-till system on soil physicochemical properties and bacterial communities at different soil depths are still unclear. In this 12-year experiment of straw removal (CK) and straw mulching (SM) treatments, soil samples were collected at 0–5, 5–10, 10–20, and 20–30 cm soil depths. The results showed that the contents of organic carbon (C), nitrogen (N), and phosphorus (P) fractions, and bacterial abundance significantly decreased, whereas pH significantly increased with soil depth. Compared with CK, SM significantly increased total N, inorganic N, available P, available potassium, and soil water content at 0–5 cm, total organic C content at 0–10 cm, and dissolved organic C and N contents at 0–20 cm. Regarding bacterial communities, SM increased the relative abundances of Proteobacteria, Bacteroidetes, and Acidobacteria but reduced those of Actinobacteria, Chloroflexi, and Cyanobacteria. Bacterial Shannon diversity and Shannon's evenness at 0–5 cm were reduced by SM treatment compared to CK treatment. Furthermore, SM increased the relative abundances of some C-cycling genera (such as Terracidiphilus and Acidibacter) and N-cycling genera (such as Rhodanobacter, Rhizomicrobium, Dokdonella, Reyranella, and Luteimonas) at 0–5 cm. Principal coordinate analysis showed that the largest difference in the composition of soil bacterial communities between CK and SM occurred at 0–5 cm. Soil pH and N and organic C fractions were the major drivers shaping soil bacterial communities. Overall, SM treatment is highly recommended under a no-till system because of its benefits to soil fertility and bacterial abundance.