Different Effects of Soil Fertilization on Bacterial Community Composition in the Penicillium canescens Hyphosphere and in Bulk Soil

Deciphering insights into rhizospheric microbial community and soil parameters under the influence of herbicides in zero-tillage tropical rice-agroecosystem

Extensive use of chemicals like herbicides in rice and other fields to manage weeds is expected to have a lasting influence on the soil environment. Considering this rationale, we aimed to decipher the effects of herbicides, Pendimethalin and Pretilachlor, applied at 0.5 and 0.6 kg ha-1, respectively on the rhizosphere microbial community and soil characteristics in the tropical rice field, managed under zero tillage cultivation. The quantity of herbicide residues declined gradually since application up to 60 days thereafter it reached the non-detectable level. Most of the soil variables viz., microbial biomass, soil enzymes etc., exhibited slight reduction in the treated soils compared to the control. A gradual decline was observed in Mineral-N, MBC, MBN and enzyme activities. Quantitative polymerase chain reaction results showed maximal microbial abundance of bacteria, fungi and archaea at mid-flowering stage of rice crop. The 16 rRNA and ITS region targeted amplicons high throughput sequencing microbial metagenomic approach revealed total of 94, 1353, and 510 species for archaea, bacteria and fungi, respectively. The metabarcoding of core microbiota revealed that the archaea comprised of Nitrososphaera, Nitrosocosmicus, and Methanosarcina. In the bacterial core microbiome, Neobacillus, Nitrospira, Thaurea, and Microvigra were found as the predominant taxa. Fusarium, Clonostachys, Nigrospora, Mortierella, Chaetomium, etc., were found in core fungal microbiome. Overall, the study exhibited that the recommended dose of herbicides found to be detrimental to the microbial dynamics, though a negative relation between residues and soil variables was observed that might alter the microbial diversity. The outcomes offer a comprehensive understanding of how herbicides affect the microbial community in zero tillage rice soil, thus has a critical imputation for eco-friendly and sustainable rice agriculture. Further, the long-term studies will be helpful in elucidating the role of identified microbial groups in sustaining the soil fertility and crop productivity.

Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria

Metabolic cross-feeding is a pervasive microbial interaction type that affects community stability and functioning and directs carbon and energy flows. The mechanisms that underlie these interactions and their association with metal/metalloid biogeochemistry, however, remain poorly understood. Here, we identified two soil bacteria, Bacillus sp. BP-3 and Delftia sp. DT-2, that engage in a two-tiered mutualism. Strain BP-3 has low utilization ability of pyruvic acid while strain DT-2 lacks hexokinase, lacks a phosphotransferase system, and is defective in glucose utilization. When strain BP-3 is grown in isolation with glucose, it releases pyruvic acid to the environment resulting in acidification and eventual self-killing. However, when strain BP-3 is grown together with strain DT-2, strain DT-2 utilizes the released pyruvic acid to meet its energy requirements, consequently rescuing strain BP-3 from pyruvic acid-induced growth inhibition. The two bacteria further enhance their collective competitiveness against other microbes by using arsenic as a weapon. Strain DT-2 reduces relatively non-toxic methylarsenate [MAs(V)] to highly toxic methylarsenite [MAs(III)], which kills or suppresses competitors, while strain BP-3 detoxifies MAs(III) by methylation to non-toxic dimethylarsenate [DMAs(V)]. These two arsenic transformations are enhanced when strains DT-2 and BP-3 are grown together. The two strains, along with their close relatives, widely co-occur in soils and their abundances increase with the soil arsenic concentration. Our results reveal that these bacterial types employ a two-tiered mutualism to ensure their collective metabolic activity and maintain their ecological competitive against other soil microbes. These findings shed light on the intricateness of bacterial interactions and their roles in ecosystem functioning.

Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature

The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.

Soil Microbial Legacy Overrides the Responses of a Dominant Grass and Nitrogen-Cycling Functional Microbes in Grassland Soil to Nitrogen Addition

Both atmospheric nitrogen (N) deposition and soil microbial legacy (SML) can affect plant performance, the activity of soil N-cycling functional microbes and the relative abundance of N-cycling functional genes (NCFGs). In the grassland vegetation successional process, how the interaction of SML and N deposition affects the performance of dominant grass and NCFGs remains unclear. Therefore, we planted Leymus chinensis, a dominant grass in the Songnen grassland, in the soil taken from the early, medium, late, and stable successional stages. We subjected the plants to soil sterilization and N addition treatments and measured the plant traits and NCFG abundances (i.e., nifH, AOB amoA, nirS, and nirK). Our results showed the biomass and ramet number of L. chinensis in sterilized soil were significantly higher than those in non-sterilized soil, indicating that SML negatively affects the growth of L. chinensis. However, N addition increased the plant biomass and the AOB amoA gene abundance only in sterilized soils, implying that SML overrode the N addition effects because SML buffered the effects of increasing soil N availability on NCFGs. Therefore, we emphasize the potential role of SML in assessing the effects of N deposition on dominant plant performance and NCFGs in the grassland vegetation succession.

Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization

Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere-bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.

Bloom of tetracycline resistance genes in mudflats following fertilization is attributed to the increases in the shared potential hosts between soil and organic fertilizers

A field experiment was carried out in mudflats adjacent to the Yellow Sea, China, amended with sewage sludge and vermicompost by one-time input at different rates to reveal the fates of tetracycline resistance genes (TRGs) and their potential hosts in the soils. Quantitative PCR results showed that soils added with either sludge or vermicompost had more abundant TRGs compared with the non-fertilized soil. This situation was more obvious in sludge fertilized soils especially at high application rates. Vermicompost exhibited a promising outlook for improvement of the mudflats. The abundances of intI1 in the non-fertilized soils were significantly higher than those in fertilizers and fertilized soils. The potential hosts for intI1 were not shared with other TRGs-contained hosts, indicating that intI1 had little effects on the dissemination of TRGs in the mudflats. Moreover, the exclusive hosts for TRGs in fertilizers were not higher than those in the non-fertilized soils, illustrating little effects of fertilization on the introduction of exogenous TRGs into soil. The shared hosts between soil and fertilizers were highest among four possible sources, contributing vastly to the bloom of TRGs following fertilization. It was also shown that different organic fertilizers caused distinct categories of shared potential hosts for TRGs. RDA analysis further indicated that the abundances of the shared potential hosts were affected by soil nutrients. These results suggested that the development of TRGs in soil following fertilization depended on the shared potential hosts with similar ecological niches between soil and fertilizers.

OUP accepted manuscript

During germination, the seed releases nutrient-rich exudates into the spermosphere, thereby fostering competition between resident microorganisms. However, insight into the composition and temporal dynamics of seed-associated bacterial communities under field conditions is currently lacking. This field study determined the temporal changes from 11 to 31 days after sowing in the composition of seed-associated bacterial communities of winter wheat as affected by long-term soil fertilization history, and by introduction of the plant growth-promoting microbial inoculants Penicillium bilaiae and Bacillus simplex. The temporal dynamics were the most important factor affecting the composition of the seed-associated communities. An increase in the relative abundance of genes involved in organic nitrogen metabolism (ureC and gdhA), and in ammonium oxidation (amoA), suggested increased mineralization of plant-derived nitrogen compounds over time. Dynamics of the phosphorus cycling genes ppt, ppx and cphy indicated inorganic phosphorus and polyphosphate cycling, as well as phytate hydrolysis by the seed-associated bacteria early after germination. Later, an increase in genes for utilization of organic phosphorus sources (phoD, phoX and phnK) indicated phosphorus limitation. The results indicate that community temporal dynamics are partly driven by changed availability of major nutrients, and reveal no functional consequences of the added inoculants during seed germination.

Characterization of soils conducive and non-conducive to Prunus replant disease

Successive orchard plantings of almond and other Prunus species exhibit reduced growth and yield in many California soils. This phenomenon, known as Prunus replant disease (PRD), can be prevented by preplant soil fumigation or anaerobic soil disinfestation, but its etiology is poorly understood and its incidence and severity are hard to predict. We report here on relationships among physicochemical variables, microbial community structure, and PRD induction in 25 diverse replant soils from California. In a greenhouse bioassay, soil was considered to be "PRD-inducing" when growth of peach seedlings in it was significantly increased by preplant fumigation and pasteurization, compared to an untreated control. PRD was induced in 18 of the 25 soils, and PRD severity correlated positively with soil exchangeable-K, pH, %clay, total %N, and electrical conductivity. The structure of bacterial, fungal, and oomycete communities differed significantly between the PRD-inducing and non-inducing soils, based on PERMANOVA of Bray Curtis dissimilarities. Bacterial class MB-A2-108 of phylum Actinobacteria had high relative abundances among PRD-inducing soils, while Bacteroidia were relatively abundant among non-inducing soils. Among fungi, many ASVs classified only to kingdom level were relatively abundant among PRD-inducing soils whereas ASVs of Trichoderma were relatively abundant among non-inducing soils. Random forest classification effectively discriminated between PRD-inducing and non-inducing soils, revealing many bacterial ASVs with high explanatory values. Random forest regression effectively accounted for PRD severity, with soil exchangeable-K and pH having high predictive value. Our work revealed several biotic and abiotic variables worthy of further examination in PRD etiology.

Nutrient load acts as a driver of gut microbiota load, community composition and metabolic functionality in the simulator of the human intestinal microbial ecosystem

A recently introduced quantitative framework for gut microbiota analysis indicated that microbial load alterations can be linked to various diseases, making it essential to pinpoint its determinants. We identified nutrient load as a main driver of the quantitative microbial community composition and functionality in vitro by stepwise decreasing standardised feed concentrations from 100% to 33, 20 and 10% in five-day intervals. While the proportional composition and metabolic profile were mainly determined by the inter-individual variability (35 and 41%), nutrient load accounted for 58%, 23% and 65% of the observed variation in the microbial load, quantitative composition and net daily metabolite production, respectively. After the tenfold nutrient reduction, the microbial load decreased by 79.72 ± 9% and 82.96 ± 1.66% in the proximal and distal colon, respectively, while the net total short-chain fatty acid production dropped by 79.42 ± 4.42% and 84.58 ± 2.42%, respectively. The majority of microbial taxa quantitatively decreased, whereas a select group of nutritional specialists, such as Akkermansia muciniphila and Bilophila wadsworthia and a number of opportunistic pathogens remained unaffected. This shows that nutrient load is an important driver of the human gut microbiome and should be considered in future in vitro and in vivo dietary research.

Comparison of the effects of acetic acid bacteria and lactic acid bacteria on the microbial diversity of and the functional pathways in dough as revealed by high-throughput metagenomics sequencing

Knowledge of the effects of various strains of acetic acid bacteria (AAB) on sourdough remains limited. In this study, the diversity of microbial taxa in sourdoughs fermented by different starters was assessed and their functional capacity was evaluated via high-throughput metagenomics sequencing. Results showed that Erwinia (29.43%), Pantoea (45.89%), and Enterobacter (9.16%) were predominant in the blank CK treatment. Lactobacillus (91.40%), Saccharomyces (6.13%), as well as the AAB genus Acetobacter (0.61%) were the dominant microbial genera in the sourdoughs started by yeast and a strain of lactic acid bacteria (YL treatment). By contrast, the dominant genera in the sourdoughs started by yeasts and various LAB and AAB strains (YLA treatment) were Komagataeibacter (0.39%) except for the inoculated Lactobacillus (68.37%), Acetobacter (20.17%), and Saccharomyces (8.31%) species. Functional prediction of these changes in microbial community and diversity revealed that various metabolism-related pathways, including alanine, aspartate, and glutamate metabolism (21.95%), as well as amino acid biosynthesis (19.14%), were predominant in the sourdoughs started by yeast and an AAB strain (YA treatment). Moreover, arginine biosynthesis (11.65%) were the dominant pathways in the YL treatment. The fermented dough added with sourdoughs started with yeast + AAB and yeast + AAB + LAB strains had substantially higher contents (more than 48.58% in total) of essential amino acids than the dough added with sourdoughs started with yeast + LAB strain. These results demonstrated that amino acid biosynthesis has a beneficial effect on sourdoughs inoculated with an AAB strain.