Effects of Cover Crop and Tillage Method Combinations on the Microbiological Traits of Spring Wheat (Triticum aestivum L.)

We carried out multivariate characterisation of phenotypic variability in 27 treatments that were combinations of cover crop, tillage method, and year. Canonical variate analysis was employed to observe nine microbiological traits in an experiment established in a split-plot design. Between 2011–2013, a field experiment was conducted on soils classified as Albic Luvisols. The first-order factor was analysis of the effect of sowing a stubble cover crop: (Control: No cover crop sown; cover crop sown after skimming; no tillage: Cover crop sown directly). The second experimental factor involved evaluating the effects of three tillage methods (direct sowing; simplified tillage to a depth of 12–15 cm with a combined cultivator; spring ploughing to a depth of 25 cm) on nine microbiological traits. The year of research was used as a factor to differentiate between the count and activity of soil microorganisms. The traits (moulds and copiotrophic bacteria, and oligotrophic bacteria and actinobacteria) were significantly correlated (positively or negatively) at all five terms. Pearson’s test confirmed the relationships between the physiological groups of soil microorganisms after the application of organic matter, and captured the positive correlation between moulds and copiotrophs at all terms of the study.

Microbiome of the Rhizosphere: from Structure to Functions

Microbial composition and functioning in the rhizosphere are among the most fascinating but hidden topics in microbial ecology. We generalized bacterial traits regarding community diversity, composition and functions using published 16s rDNA amplicon sequences of 584 pairs of bulk soils vs rhizosphere of crops. The lower bacterial diversity in the rhizosphere (-7% richness) compared to root-free soil reflects the excess of available organic substances near the root. The rhizosphere is enriched by Bacteroidetes, Proteobacteria and Cyanobacteria as well as other copiotrophic bacteria (r strategists). Complex but unstable bacterial networks in rhizosphere reflect tight microbial interactions and adaptations to fluctuating conditions common for r strategists. The dominant dormancy strategy in the rhizosphere is the toxin-antitoxin system, while sporulation is common in bulk soil. Function prediction analysis showed that the rhizosphere is strongly enriched (50–115%) in methanol oxidation, ureolysis, cellulolysis, chitinolysis and nitrogen fixation, but strongly depleted in functions related to N-cycling.

Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition

This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.

Crop rotation alleviates replant failure in Panax notoginseng (Burkill) F. H. Chen by changing the composition but not the structure of the microbial community

Consecutive monocropping with sanqi (Panax notoginseng (Burkill) F. H. Chen) can increase the abundances of pathogens in soil, resulting in soil sickness. Crop rotation is one way to alleviate this problem. In the present study, there were no differences in microbial structure or bacterial alpha diversity among one-year monocropping soil, one-year rotation soil, and ten-year rotation soil. However, monocropping practices decreased fungal alpha diversity. The relative abundance of copiotrophic bacteria decreased after sanqi monocropping, while that of oligotrophic bacteria increased. Ten-year rotation significantly increased the abundance of potential beneficial bacterial genera. Moreover, the potential beneficial fungal genera were also enriched by rotation for ten years. Furthermore, the relative abundance of Cylindrocarpon spp. decreased dramatically after a ten-year rotation. The results of pot experiments showed that disease incidences after ten-year rotation were significantly decreased among the three treatments. Hence, we suggested that pausing sanqi cultivation for a long time can increase the abundance of potentially beneficial soil bacteria and fungi that are helpful for overcoming soil sickness in sanqi cultivation.

Effects of Different Fertilizers on Rhizosphere Bacterial Communities of Winter Wheat in the North China Plain

The application of bioorganic fertilizer affects rhizosphere microbes and further improves soil fertility in farmlands. However, the effects of different fertilizers on rhizosphere bacterial community diversity and structure of winter wheat remains unclear. In this study, we explored the effects of different fertilization treatments (no fertilizer added, CK; nitrogen fertilizer, NF; bioorganic fertilizer, BOF) on the rhizosphere bacterial community of winter wheat in the North China Plain. Rhizosphere soil treated with BOF had a higher Shannon index than that of CK and NF. The relative abundance of the Proteobacteria treated with BOF was significantly higher than that of NF, while the Acidobacteria and Planctomycetes were significantly lower. The redundancy analysis (RDA) and Mantel test showed that soil bacterial communities were significantly correlated with pH, nitrate, available phosphorus (AP), and available potassium (AK). Our findings indicated that BOF increased bacterial diversity and the relative abundance of copiotrophic bacteria in rhizosphere soil, while NF reduced bacterial diversity and increased the relative abundance of oligotrophic bacteria. The increase in copiotrophic bacteria in the rhizosphere of winter wheat could indicate an increase in soil nutrient availability, which might have positive implications for soil fertility and crop production.

Response of chemical and microbial properties to short-term biochar amendment in different agricultural soils

The objective of this study was to assess the effect of biochar soil amendment (BSA) on chemical and microbial properties in different agricultural soils in Vojvodina Prov?ince. Short-term pot experiment consisted of five biochar application doses (0, 0.5, 1, 2, and 3%) and five contrasting soil types (Mollic Gleysol, Eutric Cambisol, Calcaric Fluvisol, Gleyic Chernozem, and Haplic Chernozem), planted with sunflower (Helianthus annuus L.) and winter wheat (Triticum aestivum L.). The examined chemical and microbial properties were significantly influenced by soil type and interaction of experimental factors. Significant influence of biochar on the contents of calcium carbonate (CaCO3), total nitrogen (N), total carbon (C), soil organic carbon (SOC), humus and potassium (K) of the tested soils was observed. Biochar also significantly affected the number of azotobacters (AZB), fungi (FNG), actino?mycetes (ACT) and copiotrophic bacteria (CB). The effect of BSA varied depending on the applied dose, with higher values of the examined chemical and microbial parameters at higher doses of application. Further studies on using biochar in soils with low fertility will be neces?sary to establish its efficiency as an enhancer for agricultural production in Serbia.

Co-culture and biogeography of Prochlorococcus and SAR11

Prochlorococcus and SAR11 are among the smallest and most abundant organisms on Earth. With a combined global population of about 2.7 x 1028 cells, they numerically dominate bacterioplankton communities in oligotrophic ocean gyres and yet they have never been grown together in vitro. Here we describe co-cultures of Prochlorococcus and SAR11 isolates representing both high- and low-light adapted clades. We examined: (1) the influence of Prochlorococcus on the growth of SAR11 and vice-versa, (2) whether Prochlorococcus can meet specific nutrient requirements of SAR11, and (3) how co-culture dynamics vary when Prochlorococcus is grown with SAR11 compared with sympatric copiotrophic bacteria. SAR11 grew as much as 70% faster in the presence of Prochlorococcus, while the growth of the latter was unaffected. When Prochlorococcus populations entered stationary phase, SAR11 abundances decreased dramatically. In parallel experiments with copiotrophic bacteria however, the heterotrophic partner increased in abundance as Prochlorococcus densities leveled off. The presence of Prochlorococcus was able to meet SAR11’s central requirement for organic carbon, but not reduced sulfur. Prochlorococcus strain MIT9313, but not MED4, could meet the unique glycine requirement of SAR11, likely due to production and release of glycine betaine by MIT9313. Evidence suggests that Prochlorococcus MIT9313 may also compete with SAR11 for the uptake of 3-dimethylsulfoniopropionate (DMSP). To place our results in context, we assessed the relative contribution of Prochlorococcus and SAR11 genome equivalents to those of identifiable bacteria and archaea in over 800 marine metagenomes. At many locations, more than half of the identifiable genome equivalents in the euphotic zone belonged to Prochlorococcus and SAR11 – highlighting the biogeochemical potential of these two groups.

Free-living Bacterial Communities Are Mostly Dominated by Oligotrophs

In response to resource availability, bacteria have evolved two distinct ecological strategies. Copiotrophic bacteria grow fast and are heavily favored by selection where the resource is abundant. In contrast, oligotrophic bacteria grow slowly but more efficiently and are highly adaptive in nutrient-poor environments (Koch, 2001). Although oligotrophs and copiotrophs are ubiquitous, except for a few well-characterized environments like the open ocean and animal gut, the relative abundance of oligotrophic and copiotrophic bacteria and their importance in the global ecosystem are still unclear. In addition, although several studies have demonstrated the impact of nutrient availability on the bacterial community structure under experimental conditions (Klappenbach et al., 2000, Nemergut et al., 2016), the role of nutrients in shaping the structures of bacterial communities in their natural habitats remains largely unknown. Using the ribosomal RNA operon (rrn) copy number to capture the bacterial ecological strategy, we analyzed 44,045 samples from two large bacterial community repositories that cover 78 environmental types. Here we show that animal-associated microbiota are dominated by copiotrophs while plant-associated and free-living bacterial communities are mostly dominated by oligotrophs. Our results suggest that nutrient availability plays an important role in determining the structure and ecological strategy of bacterial communities in nature. We demonstrate that the average and distribution of rrn copy number are simple yet robust predictors of the ecological strategy of bacterial communities that can be applied to all sequence-based microbial surveys to link the community structure and function.

THE EFFECT OF NITROGEN ON THE MICROBIOLOGICAL AND BIOCHEMICAL PROPERTIES OF ZINC-CONTAMINATED SOIL

The aim of these studies was to determine the influence of excessive zinc doses on the microbiological and enzymatic properties of soil. Also, an evaluation of the possibility to stimulate remediation processes by nitrogen fertilisation of the soil was attempted. Zinc was applied to loamy sand in the amounts of 0, 250, 500, 750, 1000, 1250 mg Zn2+ kg–1 DM soil, while nitrogen in the form of urea in doses of 0, 250, 500 mg N kg–1 DM soil. Soil samples were incubated at a temperature of 25 °C, maintaining a constant humidity equal to 50% of the maximum water capacity. In the 2nd and 20th week of the experiment, the following factors were determined: activity of dehydrogenases and catalase, and number of organotrophic bacteria, copiotrophic bacteria, oligotrophic bacteria, actinomycetes, and fungi. Zinc inhibited the enzymatic activity of the soil, while causing a slight increase in populations of microorganisms. Only fungi reacted unequivocally positively to contamination of the soil with zinc, therefore demonstrating changes in the biodiversity of microorganisms. Nitrogen fertilisation of the soil resulted in stabilization of the environment contaminated with zinc by stimulation of growth of microorganisms resistant to the influence of this metal.