scholarly journals Peer Review #1 of "Effects of fertilizations on soil bacteria and fungi communities in a degraded arid steppe revealed by high through-put sequencing (v0.1)"

2018 ◽  
Keyword(s):  
Peer Review ◽  
Soil Bacteria ◽  
Arid Steppe ◽  
Soil Bacteria And Fungi ◽  
Bacteria And Fungi

scholarly journals Effects of fertilizations on soil bacteria and fungi communities in a degraded arid steppe revealed by high through-put sequencing

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4623 ◽  
Author(s):  
Luhua Yao ◽  
Dangjun Wang ◽  
Lin Kang ◽  
Dengke Wang ◽  
Yong Zhang ◽  
...  
Keyword(s):  
Microbial Biomass ◽  
Soil Properties ◽  
Soil Bacteria ◽  
Microbial Biomass Carbon ◽  
Chemical Properties ◽  
Soil Chemical Properties ◽  
Microbial Biomass Nitrogen ◽  
Arid Steppe ◽  
Soil Bacteria And Fungi ◽  
Bacteria And Fungi

Background Fertilization as one of the measures in restoring degraded soil qualities has been introduced on arid steppes in recent decades. However, the fertilization use efficiency on arid steppes varies greatly between steppe types and years, enhancing uncertainties and risks in introducing fertilizations on such natural system to restore degraded steppes. Methods The experiment was a completely randomized design with five fertilization treatments, 0 (Control), 60 kg P ha−1 (P), 100 kg N ha−1 (N), 100 kg N ha−1 plus 60 kg P ha−1 (NP), and 4,000 kg sheep manure ha−1 (M, equaling 16.4 kg P ha−1 and 81.2 kg N ha−1). Soils were sampled from a degraded arid steppe which was consecutively applied with organic and inorganic fertilizers for three years. We analyzed the diversity and abundance of soil bacteria and fungi using high-throughput sequencing technique, measured the aboveground biomass, the soil chemical properties (organic carbon, available and total phosphorus, available and total nitrogen, and pH), and the microbial biomass nitrogen and microbial biomass carbon. Results In total 3,927 OTU (operational taxonomic units) for bacteria and 453 OTU for fungi were identified from the tested soils. The Ace and Chao of bacteria were all larger than 2,400, which were almost 10 times of those of fungi. Fertilizations had no significant influence on the richness and diversity of the bacteria and fungi. However, the abundance of individual bacterial or fungi phylum or species was sensitive to fertilizations. Fertilization, particularly the phosphorus fertilizer, influenced more on the abundance of the AMF species and colonization. Among the soil properties, soil pH was one of the most important soil properties influencing the abundance of soil bacteria and fungi. Discussion Positive relationships between the abundance of bacteria and fungi and the soil chemical properties suggested that soil bacteria and fungi communities in degraded steppes could be altered by improving the soil chemical properties through fertilizations. However, it is still not clear whether the alteration of the soil microbe community is detrimental or beneficial to the degraded arid steppes.

scholarly journals Transcription of protease and chitinase genes provides a window onto macromolecular organic nitrogen decomposition in soil

2020 ◽  
Author(s):  
Ella T. Sieradzki ◽  
Erin E. Nuccio ◽  
Jennifer Pett-Ridge ◽  
Mary K. Firestone
Keyword(s):  
Soil Bacteria ◽  
Extracellular Enzymes ◽  
Plant Litter ◽  
Organic Substrates ◽  
Extracellular Proteases ◽  
Carbon And Nitrogen ◽  
Limiting Nutrient ◽  
Soil Bacteria And Fungi ◽  
Bacteria And Fungi ◽  
Chitinase Genes

AbstractNitrogen is a common limiting nutrient in soil in part because most N is present as macromolecular organic compounds, not directly available to plants. The microbial community present in soil near roots (rhizosphere) is in many ways analogous to the human gut microbiome, transforming nutrients present in organic substrates to forms available to plants through extracellular enzymes. Many recent studies have focused on the genetic potential for nitrogen cycling by bacteria in the rhizosphere, and on measuring inorganic N pools and fluxes. Between those two bodies of knowledge, there is scarce information on functionality of macromolecular nitrogen decomposing bacteria and fungi and how it relates to life stages of the plant. This is particularly important as many soil bacteria identified in community composition studies can be inactive or not viable. Here we use a time-series of metatranscriptomes from rhizosphere and bulk soil bacteria and fungi to follow extracellular protease and chitinase expression during rhizosphere aging. In addition, we explore the effect of adding plant litter as a source of macromolecular carbon and nitrogen. Expression of extracellular proteases increased over time in the absence of litter, more so in the presence of roots, whereas the dominant chitinase (chit1) was upregulated with exposure to litter. Structural groups of proteases were surprisingly dominated by serineproteases, possibly due to the importance of betaproteobacteria and actinobacteria in this grassland soil. Extracellular proteases of betaprotebacterial origin were more highly expressed in the presence of roots, whereas deltaroteobacteria and fungi responded to the presence of litter. We found functional guilds specializing in decomposition of proteins in the rhizosphere, detritusphere and in the vicinity of aging roots. We also identify a guild that appears to specialize in protein decomposition in the presence of roots and litter and increases its activity in aging rhizosphere, which may imply that this guild targets rhizodeposits or the senescing root itself as a protein source. Different temporal patterns of guilds imply that rather than functional redundancy, microbial decomposers operate within distinct niches.

scholarly journals The Influence of Climate Warming and Humidity on Plant Diversity and Soil Bacteria and Fungi Diversity in Desert Grassland

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2580
Author(s):  
Yi Zhang ◽  
Yingzhong Xie ◽  
Hongbin Ma ◽  
Juan Zhang ◽  
Le Jing ◽  
...  
Keyword(s):  
Plant Diversity ◽  
Soil Bacteria ◽  
Interactive Effects ◽  
Desert Grassland ◽  
Plant Soil ◽  
Β Diversity ◽  
Temperature And Precipitation ◽  
Α Diversity ◽  
Soil Bacteria And Fungi ◽  
Bacteria And Fungi

Our study, which was conducted in the desert grassland of Ningxia in China (E 107.285, N 37.763), involved an experiment with five levels of annual precipitation 33% (R33), 66% (R66), 100% (CK), 133% (R133), 166% (R166) and two temperature levels (inside Open-Top Chamber (OTC) and outside OTC). Our objective was to determine how plant, soil bacteria, and fungi diversity respond to climate change. Our study suggested that plant α-diversity in CK and TCK were significantly higher than that of other treatments. Increased precipitation promoted root biomass (RB) growth more than aboveground living biomass (ALB). R166 promoted the biomass of Agropyron mongolicum the most. In the fungi communities, temperature and precipitation interaction promoted α-diversity. In the fungi communities, the combination of increased temperature and natural precipitation (TCK) promoted β-diversity the most, whose distance was determined to be 25,124 according to PCA. In the bacteria communities, β-diversity in CK was significantly higher than in other treatments, and the distance was determined to be 3010 according to PCA. Soil bacteria and fungi α- and β-diversity, and ALB promoted plant diversity the most. The interactive effects of temperature and precipitation on C, N, and P contents of plants were larger than their independent effects.

scholarly journals Streptomycesvolatile compounds influence exploration and microbial community dynamics by altering iron availability

2018 ◽  
Author(s):  
Stephanie E. Jones ◽  
Christine A. Pham ◽  
Joseph McKillip ◽  
Matthew Zambri ◽  
Erin E. Carlson ◽  
...  
Keyword(s):  
Soil Bacteria ◽  
Community Dynamics ◽  
Critical Role ◽  
Iron Chelators ◽  
Iron Availability ◽  
Microbial Community Dynamics ◽  
Volatile Organic ◽  
Soil Bacteria And Fungi ◽  
New Form ◽  
Bacteria And Fungi

ABSTRACTBacteria and fungi produce a wide array of volatile organic compounds (VOCs), and these can act as infochemicals or as competitive tools. Recent work has shown that the VOC trimethylamine (TMA) can promote a new form ofStreptomycesgrowth, termed ‘exploration’. Here, we report that TMA also serves to alter nutrient availability in the area surrounding exploring cultures: TMA dramatically increases the environmental pH, and in doing so, reduces iron availability. This, in turn, compromised the growth of other soil bacteria and fungi. In contrast,Streptomycesthrives in these iron-depleted niches by secreting a suite of differentially modified siderophores, and by upregulating genes associated with siderophore uptake. Further reducing iron levels by siderophore piracy, limiting siderophore uptake, or growing cultures in the presence of iron chelators, unexpectedly enhanced exploration. Our work reveals a new role for VOCs in modulating iron levels in the environment, and implies a critical role for VOCs in modulating the behaviour of microbes and the makeup of their communities.

scholarly journals Consistent effects of vegetation loss on abundant and rare soil microbial phylotypes across nitrogen-enrichment levels

2019 ◽  
Author(s):  
Dima Chen ◽  
Ying Wu ◽  
Muhammad Saleem ◽  
Bing Wang ◽  
Shuijin Hu ◽  
...  
Keyword(s):  
Soil Bacteria ◽  
Alpha Diversity ◽  
N Deposition ◽  
Bacterial Phylotypes ◽  
Soil Microbial ◽  
N Enrichment ◽  
Soil Bacteria And Fungi ◽  
Bacteria And Fungi ◽  
Vegetation Loss ◽  
First Time

Abstract Soil harbors highly diverse abundant and rare microbial phylotypes that drive multiple soil functions. Given increasing intensity and frequency of vegetation loss and anthropogenic reactive nitrogen (N) inputs to the soil in the future, we lack a mechanistic understanding of how vegetation loss may influence abundant and rare microbial phylotypes at various N-enrichment levels. In the current study, we assessed the effects of vegetation loss on abundant and rare phylotypes of soil bacteria and fungi across three N-enrichment levels in a semi-arid grassland ecosystem. After six years of experimentation in with and without vegetation plots, the vegetation loss increased the total relative abundance of abundant soil bacterial phylotypes but not that of abundant fungal phylotypes at across N-enrichment levels. It is very likely because the number of abundant bacterial phylotypes with positive than negative responses to vegetation loss was higher; however, the number of abundant fungal phylotypes with positive than negative responses to vegetation loss was similar during this period. Moreover, the vegetation loss did not alter the alpha-diversity of abundant or rare bacterial phylotypes, or, of abundant fungal phylotypes; however, it reduced the alpha-diversity of rare fungal phylotypes at across N-enrichment levels. The vegetation loss, however, altered the beta-diversity of abundant and rare bacterial and fungal phylotypes across N-enrichment levels. We found that, against expectations, the effects of vegetation loss on the diversity of abundant and rare phylotypes of both bacteria and fungi were relatively consistent across N-enrichment levels. Our findings provide, for the first time, the phylotype-based data on how vegetation loss affects abundant and rare phylotypes of soil bacteria and fungi across N-enrichment levels. The results also indicate that the effects of vegetation loss on belowground functions may be relatively insensitive to the differences in the N-deposition rates.

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