Long-term cropping rotation with soybean enhances soil health as evidenced by improved nutrient cycles through keystone phylotypes interaction

We estimated the effect of three crop strategies on soil health based on 63 functional genes in long-term fields.The keystone microbial phylotypes support the agroecosystem sustainability.Rotation management thrives keystone phylotypes and soil functions.Rotation with soybean is beneficial for the subsequent crops.Given the often-independent study of microbial diversity and function,the comprehensive impact of various cropping patterns on both aspects,as well as the interconnections between them,remains unclear.This gap constrains us from evaluating the impact of soil microbiome shifts on soil health across varying agricultural management regimes.Here,we examined the associations between microbial diversity and soil multifunctionality in three long-term cropping patterns:continuous soybean cropping,soybeancorn rotation,and continuous corn cropping.We targeted 63 functional genes associated with carbon,nitrogen,phosphorus and sulfur cycling to assess soil multifunctionality.Our study demonstrated that the biodiversity and interactions of keystone phylotypes had significant positive associations with multiple soil functional genes,such as organic carbon degradation and fixation,nitrogen fixation and phosphorus solubilization.The analysis of retrieved complete genome revealed that the keystone bacteria identified in our study harbored these functional genes.Moreover,these keystone phylotypes showed associations with the dissipation of herbicide residues.Above all,we revealed that rotation of soybean with corn cropping enhanced a greater diversity of keystone phylotypes and thus fueled soil functions.Collectively,our results highlighted the importance of rotation with soybean in maintaining soil health,which could give a mechanism-based guidance for a sustainable agroecosystem.

Phylotype resolved spatial variation and association patterns of planktonic Thaumarchaeota in eastern Chinese marginal seas

The majority of marine ammonia oxidizers belong to Thaumarchaeota,a phylum of Archaea,which is distributed throughout the water column.Marine surface waters contain distinct thaumarchaeotal phylotypes compared to the deeper ocean,but spatial dynamics of the surface-associated lineages are largely unsolved.This study of 120 seawater samples from the eastern Chinese marginal seas identifed contrasting distribution and association patterns among thaumarchaeotal phylotypes across diferent dimensions.Horizontally,Nitrosopumilus-like and Nitrosopelagicus-like phylotypes dominated the surface water(3 m)of the Yellow Sea(YS)and East China Sea(ECS),respectively,along with increased abundance of total free-living Thaumarchaeota in ECS.Similar compositional changes were observed in the surface microlayer.The spatial heterogeneity of particle-attached Thaumarchaeota was less clear in surface microlayers than in surface waters.Vertically,the Nitrosopelagicus-like phylotype increased in abundance from surface to 90 m in ECS,which led to an increase in the proportion of Thaumarchaeota relative to total prokaryotes.This occurred mainly in the free-living fraction.These results indicate a clear size-fractionated niche partitioning,which is more pronounced at lower depths than in the surface water/surface microlayer.In addition,associations of Thaumarchaeota with other microbial taxa varied between phylotypes and size fractions.Our results show that a phylotype-resolved and size-fractionated spatial heterogeneity of the thaumarchaeotal community is present in surface oceanic waters and a vertical variation of the Nitrosopelagicus-like phylotype is present in shallow shelf waters.

Genetic Diversity of Uropathogenic Escherichia coli Isolated from Human T Lymphotropic Virus Type I (HTLV-I) Infected Individuals

Urinary tract infection (UTI) is a frequent pathology among HTLV-I+ individuals being capable of severely compromising the kidneys and bladder. Molecular characteristics of uropathogenic Escherichia coli (UPEC) from HTLV-I+ infected individuals are unknown. UPEC isolates from HTVL-I+ individuals, with and without clinical symptoms of myelopathy, were submitted to genetic typing seeking to infer bacterial diversity and potential virulence. 71 bacterial isolates were characterized according to random amplified polymorphic DNA and phylotypes. Phylotyping classified E. coli into four phylogenetic groups: A (18.3%), B1 (16.9%), B2 (39.4%), and D (25.3%) and 8 phylotypes according to the presence of the genetic sequences chuA, yjaA and the DNA fragment TSPE4.C2: ﹣﹣﹣ (5.6%) and ﹣+﹣ (12.6%) in phylogroup A, ﹣﹣+ (7.0%) and ﹣++ (9.8%) in B1, +++ (32.3%) and ++﹣ (7.0%) in B2, +﹣﹣ (15.4%) and +﹣+ (9.8%) in D. The B2 phylogroup was the most prevalent among HTLV﹣ associated myelopathy and asymptomatic individuals. RAPD-PCR typing revealed a high degree of bacterial polymorphism indicating a non-clonal origin. Genotypes were not found to be distributed according to clinical status or epidemiological features. Our results lead us to suggest that the neurological impairment in HTLV-I+ individuals can be a risk factor for urinary infections due E. coli which are caused by distinct bacterial lineages.

Green manuring relocates microbiomes in driving the soil functionality of nitrogen cycling to obtain preferable grain yields in thirty years

Fertilizers are widely used to produce more food, inevitably altering the diversity and composition of soil organisms. The role of soil biodiversity in controlling multiple ecosystem services remains unclear, especially after decades of fertilization. Here, we assess the contribution of the soil functionalities of carbon(C), nitrogen(N), and phosphorus(P) cycling to crop production and explore how soil organisms control these functionalities in a 33-year field fertilization experiment. The long-term application of green manure or cow manure produced wheat yields equivalent to those obtained with chemical N, with the former providing higher soil functions and allowing the functionality of N cycling(especially soil N mineralization and biological N fixation) to control wheat production. The keystone phylotypes within the global network rather than the overall microbial community dominated the soil multifunctionality and functionality of C,N, and P cycling across the soil profile(0–100 cm). We further confirmed that these keystone phylotypes consisted of many metabolic pathways of nutrient cycling and essential microbes involved in organic C mineralization, N_(2)O release, and biological N fixation. The chemical N, green manure, and cow manure resulted in the highest abundances of amoB, nifH, and GH48 genes and Nitrosomonadaceae,Azospirillaceae, and Sphingomonadaceae within the keystone phylotypes, and these microbes were significantly and positively correlated with N_(2)O release, N fixation, and organic C mineralization, respectively. Moreover, our results demonstrated that organic fertilization increased the effects of the network size and keystone phylotypes on the subsoil functions by facilitating the migration of soil microorganisms across the soil profiles and green manure with the highest migration rates. This study highlights the importance of the functionality of N cycling in controlling crop production and keystone phylotypes in regulating soil functions, and provides selectable fertilization strategies for maintaining crop production and soil functions across soil profiles in agricultural ecosystems.

Comparison of gut-associated and nest-associated microbial communities of a fungus-growing termite （Odontotermes yunnanensis）

The digestion of cellulose by fungus-growing termites involves a complex of different organisms, such as the termites themselves, fungi and bacteria. To further investigate the symbiotic relationships of fungus-growing termites, the microbial communities of the termite gut and fungus combs of Odontotermes yunnanensis were examined. The major fungus species was identified as Termitomyces sp. To compare the micro-organism diversity between the digestive tract of termites and fungus combs, four polymerase chain reaction clone libraries were created （two fungus-targeted internal transcribed spacer [ITS] - ribosomal DNA [rDNA] libraries and two bacteria-targeted 16S rDNA libraries）, and one library of each type was produced for the host termite gut and the symbiotic fimgus comb. Results of the fungal clone libraries revealed that only Termitomyces sp. was detected on the fungus comb; no non-Termitomyces fungi were detected. Meanwhile, the same fungus was also found in the termite gut. The bacterial clone libraries showed higher numbers and greater diversity of bacteria in the termite gut than in the fungus comb. Both bacterial clone libraries from the insect gut included Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, Nitrospira, Deferribacteres, and Fibrobacteres, whereas the bacterial clone libraries from the fungal comb only contained Firmicutes, Bacteroidetes, Proteobacteria, and Acidobacteris.

Heterotrophy-coordinated diazotrophy is associated with significant changes of rare taxa in soil microbiome

Soil heterotrophic respiration during decomposition of carbon(C)-rich organic matter plays a vital role in sustaining soil fertility.However,it remains poorly understood whether dinitrogen(N_(2))fixation occurs in support of soil heterotrophic respiration.In this study,^(15)N_(2)-tracing indicated that strong N_(2)fixation occurred during heterotrophic respiration of carbon-rich glucose.Soil organic ^(15)N increased from 0.37 atom%to 2.50 atom%under aerobic conditions and to 4.23 atom%under anaerobic conditions,while the concomitant CO_(2)flux increased by 12.0-fold under aerobic conditions and 5.18-fold under anaerobic conditions.Soil N_(2)fixation was completely absent in soils replete with inorganic N,although soil N bioavailability did not alter soil respiration.High-throughput sequencing of the 16S rRNA gene further indicated that:i)under aerobic conditions,only 15.2%of soil microbiome responded positively to glucose addition,and these responses were significantly associated with soil respiration and N_(2)fixation and ii)under anaerobic conditions,the percentage of responses was even lower at 5.70%.Intriguingly,more than 95%of these responses were originally rare with<0.5%relative abundance in background soils,including typical N_(2)-fixing heterotrophs such as Azotobacter and Clostridium and well-recognized non-N_(2)-fixing heterotrophs such as Sporosarcina,Agromyces,and Sedimentibacter.These results suggest that only a small portion of the soil microbiome could respond quickly to the amendment of readily accessible organic C in a fluvo-aquic soil and highlighted that rare phylotypes might have played more important roles than previously appreciated in catalyzing soil C and nitrogen turnovers.Our study indicates that N_(2)fixation could be closely associated with microbial turnover of soil organic C when available in excess.