Invariant community structure of soil bacteria in subtropical coniferous and broadleaved forests

ddPCR surpasses classical qPCR technology in quantitating bacteria and fungi in the environment

Quantitative real-time PCR (qPCR) has been widely used in quantifying bacterial and fungal populations in various ecosystems, as well as the fungi to bacteria ratio (F:B ratio). Recently, researchers have begun to apply droplet digital PCR (ddPCR) to this area, however, no study has systematically compared qPCR and ddPCR for quantitating both bacteria and fungi in environmental samples at the same time. Here, we designed probe-primer pair combinations targeting the 16S rRNA gene and Internal Transcribed Spacer (ITS) for the detection of bacteria and fungi respectively, and tested both SYBR Green and TaqMan approaches in qPCR and ddPCR methods for mock communities and in real environmental samples. In mock communities, the quantification results of ddPCR were significantly closer to expected values (P < 0.05), and had smaller coefficients of variations (P < 0.05) than qPCR, suggesting ddPCR was more accurate and repeatable. In environmental samples, ddPCR consistently quantified ITS and 16S rRNA gene concentrations in all four habitats without abnormal overestimation or underestimation, and the F:B ratio obtained by ddPCR was consistent with phospholipid fatty acid analysis. Our results indicated that ddPCR had better precision, repeatability, sensitivity, and stability in bacterial and fungal quantitation than qPCR. Although ddPCR has high cost, complicated processes and restricted detection range, it shows insensitivity to PCR inhibitors and the potential of quantifying long target fragments. We expect that ddPCR, which is complementary to qPCR, will contribute to microbial quantification in environmental monitoring and evaluation.

Diluted Luria-Bertani medium vs. sewage sludge as growth media: comparison of community structure and diversity in the culturable bacteria

Because colony formation is essential to seek bacterial functions by the direct observation of phenotype, the diversification of colony formation for culturable bacteria is a big challenge in the research field of Environmental Biotechnology. In this study, the biodiversity of cultivable bacteria (colony or liquid culture) was compared by using Luria-Bertani (LB) medium and waste sewage sludge (WSS) under different dilutions and temperatures. When WSS was used as a bacterial source, whereas the highest number of colonies was found at the concentration of WSS (5%), a particular concentration of LB (10%) or WSS (1%) as a growth medium showed the best number of the operational taxonomic units (OTUs) of colonies. The results of bacterial community structure indicated that there are 1, 8, and 12 bacterial genera found uniquely in the agar plates of LB, 10% LB, and 5% WSS. By contrast, when palm oil mill effluent sludge was used as a bacterial source, the effect of dilution was different with WSS. When comparing the biodiversity between colonies and liquid culture, a high OTU value was observed in the colonies on the plate. In addition, 30°C showed the highest number of colonies in LB, 10% LB, and 5% WSS whereas the best OTUs were observed at 37°C for LB and 10% LB, and at 25°C for 5% WSS. This study demonstrates the diversification of cultivable bacteria through the number of OTUs in diluted LB medium and WSS, which is beneficial to isolate a unique bacterial strain.Key points• Impacts of diluted LB medium and WSS for colony formation were determined.• Difference of concentration of LB and WSS made different effects on colony formation.• Temperature change affected on diluted LB and WSS as media.

Soil microbial community dynamics mediate the priming effects caused by in situ decomposition of fresh plant residues

Extreme climate events always leave numerous fresh plant materials (FOM) in forests, thus increasing the input of carbon (C) resources to soil system. The input of exogenous C may accelerate or inhibit the decomposition of soil organic carbon (SOC), which is defined as the positive or negative priming effect (PE), respectively. However, the characteristics and microbial mechanisms of PE caused by FOM remain unknown. A 110-day in situ soil incubation experiment was conducted in a subtropical forest, with ¹³C-labeled fresh leaves from four native species (Castanopsis fissa, CF; Pinus massoniana, PM; Machilus chekiangensis, MC; and Castanopsis chinensis, CC) serving as the FOM respectively. We measured the CO₂ effluxes derived from ¹³C-labeled FOM and soil, and the composition and diversity of soil bacterial and fungal communities throughout the incubation to explore the correlations between PE and microbial attributes. As a result, the PE caused by FOM inputs were negative initially but became positive after 61 d. The FOM decomposition rate was positively related to PE intensity, and there was a significant difference between coniferous and broadleaved species in the middle period of the study. More than 77% of the total C lost from FOM was emitted as CO₂, indicating that FOM-C serves as an energy resource for soil microbes. The α-diversity of the bacterial community at genus-level showed significantly positive correlation with PE at 24 d, and the composition of bacterial community at OTU-level had a marked relationship with the PE between 24-110 d. The relationship between fungal community diversity and composition with PE was only observed at 7 and 110 d, respectively. This study firstly investigated the patterns of PE resulted from numerous FOM input, and the results suggested that soil bacterial community, in particular the Actinobacteria phyla, played a more important role in triggering such PEs than fungal community.

The effects of organic and inorganic phosphorus amendments on the biochemical attributes and active microbial population of agriculture podzols following silage corn cultivation in boreal climate

Phosphorus (P) is the second most important macronutrient that limits the plant growth, development and productivity. Inorganic P fertilization in podzol soils predominantly bound with aluminum and iron, thereby reducing its availability to crop plants. Dairy manure (DM) amendment to agricultural soils can improve physiochemical properties, nutrient cycling through enhanced enzyme and soil microbial activities leading to improved P bioavailability to crops. We hypothesized that DM amendment in podzol soil will improve biochemical attributes and microbial community and abundance in silage corn cropping system under boreal climate. We evaluated the effects of organic and inorganic P amendments on soil biochemical attributes and abundance in podzol soil under boreal climate. Additionally, biochemical attributes and microbial population and abundance under short-term silage corn monocropping system was also investigated. Experimental treatments were [P0 (control); P1: DM with high P2O5; P2: DM with low P2O5; P3: inorganic P and five silage-corn genotypes (Fusion RR, Yukon R, A4177G3RIB, DKC 23-17RIB and DKC 26-28RIB) were laid out in a randomized complete block design in factorial settings with three replications. Results showed that P1 treatment increased acid phosphatase (AP-ase) activity (29% and 44%), and soil available P (SAP) (60% and 39%) compared to control treatment, during 2016 and 2017, respectively. Additionally, P1 treatments significantly increased total bacterial phospholipids fatty acids (ΣB-PLFA), total phospholipids fatty acids (ΣPLFA), fungi, and eukaryotes compared to control and inorganic P. Yukon R and DKC 26-28RIB genotypes exhibited higher total bacterial PLFA, fungi, and total PLFA in their rhizospheres compared to the other genotypes. Redundancy analyses showed promising association between P1 and P2 amendment, biochemical attributes and active microbial population and Yukon R and DKC 26-28RIB genotypes. Pearson correlation also demonstrated significant and positive correlation between AP-ase, SAP and gram negative bacteria (G-), fungi, ΣB-PLFA, and total PLFA. Study results demonstrated that P1 treatment enhanced biochemical attributes, active microbial community composition and abundance and forage production of silage corn. Results further demonstrated higher active microbial population and abundance in rhizosphere of Yukon R and DKC 26-28RIB genotypes. Therefore, we argue that dairy manure amendment with high P2O5 in podzol soils could be a sustainable nutrient source to enhance soil quality, health and forage production of silage corn. Yukon R and DKC 26-28RIB genotypes showed superior agronomic performance, therefore, could be good fit under boreal climatic conditions.

Coniferous-Broadleaf Mixture Increases Soil Microbial Biomass and Functions Accompanied by Improved Stand Biomass and Litter Production in Subtropical China

Although the advantages of multi-species plantations over single-species plantations have been widely recognized, the mechanisms driving these advantages remain unclear. In this study, we compared stand biomass, litter production and quality, soil properties, soil microbial community, and functions in a Pinus massoniana Lamb. and Castanopsis hystrix Miq. mixed plantation and their corresponding mono-specific plantations after 34 years afforestation in subtropical China. The results have shown that a coniferous-broadleaf mixture created significantly positive effects on stand biomass, litter production, soil microbial biomass, and activities. Firstly, the tree, shrub and herb biomass, and litter production were significantly higher in the coniferous-broadleaf mixed plantation. Secondly, although the concentrations of soil organic carbon (SOC) and total nitrogen (TN) were lower in the mixed stand, the concentrations of soil microbial biomass carbon (MBC), and nitrogen (MBN), along with MBC-to-SOC and MBN-to-TN ratio, were significantly higher in mixed stands with markedly positive admixing effects. We also found higher carbon source utilization ability and β−1, 4−N−acetylglucosaminidase, urease and acid phosphatase activities in mixed stands compared with the mono-species stands. Our results highlight that establishment of coniferous-broadleaf mixed forests may be a good management practice as coniferous-broadleaf mixture could accumulate higher stand biomass and return more litter, resulting in increasing soil microbial biomass and related functions for the long term in subtropical China.

Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland

Moisture and temperature play important roles in the assembly and functioning of prokaryotic communities in soil. However, how moisture and temperature regulate the function of niche- versus neutral-based processes during the assembly of these communities has not been examined considering both the total microbial community and the sole active portion with potential for growth in native subtropical grassland. We set up a well-controlled microcosm-based experiment to investigate the individual and combined effects of moisture and temperature on soil prokaryotic communities by simulating subtropical seasons in grassland. The prokaryotic populations with potential for growth and the total prokaryotic community were assessed by 16S rRNA transcript and 16S rRNA gene analyses, respectively. Moisture was the major factor influencing community diversity and structure, with a considerable effect of this factor on the total community. The prokaryotic populations with potential for growth and the total communities were influenced by the same assembly rules, with the niche-based mechanism being more influential in communities under dry condition. Our results provide new information regarding moisture and temperature in microbial communities of soil and elucidate how coexisting prokaryotic populations, under different physiological statuses, are shaped in native subtropical grassland soil.

Microbial communities associated with barley growing in an oil sands reclamation area in Alberta, Canada

Microbial communities that colonize the plant rhizosphere and the root interior can ameliorate plant stress and promote growth. These plant–microbe associations are being investigated to assist in reclamation soils in northern Alberta. This study assessed the diversity of bacterial species associated with barley plants growing at different cover managements and slope positions in an oil sands reclamation area. Phospholipid fatty acid analysis of the microbial communities indicated that both cover type and slope, in addition to soil total and organic carbon, NH4+, and organic matter, were significant determinants of microbial community composition. However, analysis of denaturing gel gradient electrophoresis (DGGE) banding patterns revealed that while most bulk and rhizosphere soils differentiated by cover management, no clustering was observed in endophytes. In addition, techniques to assess culture-dependent endophytic bacteria revealed a dominance of the class Gammaproteobacteria, in which Enterobacteriaceae (44%), Xanthomonaceae (30%), and Pseudomonaceae (26%) were the most abundant families in this class. Several endophytic isolates also matched those from DGGE profiles. The results of this study suggest that plants growing on oil sands reclamation covers host a wide range of bacterial endophytes, which should be assessed as to their potential to assist plant establishment and growth at such sites.

Diversity of Ktedonobacteria with Actinomycetes-Like Morphology in Terrestrial Environments

Bacteria with an actinomycetes-like morphology have recently been discovered, and the class Ktedonobacteria was created for these bacteria in the phylum Chloroflexi. They may prove to be a valuable resource with the potential to produce unprecedented secondary metabolites. However, our understanding of their diversity, richness, habitat, and ecological significance is very limited. We herein developed a 16S rRNA gene-targeted, Ktedonobacteria-specific primer and analyzed ktedonobacterial amplicons. We investigated abundance, diversity, and community structure in forest and garden soils, sand, bark, geothermal sediment, and compost. Forest soils had the highest diversity among the samples tested (1181-2934 operational taxonomic units [OTUs]; Chao 1 estimate, 2503-5613; Shannon index, 4.21-6.42). A phylogenetic analysis of representative OTUs revealed at least eight groups within unclassified Ktedonobacterales, expanding the known diversity of this order. Ktedonobacterial communities markedly varied among our samples. The common mesic environments (soil, sand, and bark) were dominated by diverse phylotypes within the eight groups. In contrast, compost and geothermal sediment samples were dominated by known ktedonobacterial families (Thermosporotrichaceae and Thermogemmatisporaceae, respectively). The relative abundance of Ktedonobacteria in the communities, based on universal primers, was ≤0.8%, but was 12.9% in the geothermal sediment. These results suggest that unknown diverse Ktedonobacteria inhabit common environments including forests, gardens, and sand at low abundances, as well as extreme environments such as geothermal areas.