scholarly journals Contrasting Soil pH Effects on Fungal and Bacterial Growth Suggest Functional Redundancy in Carbon Mineralization

2009 ◽  
Vol 75 (6) ◽  
pp. 1589-1596 ◽  
Author(s):  
Johannes Rousk ◽  
Philip C. Brookes ◽  
Erland Bååth
Keyword(s):  
Soil Ph ◽  
Bacterial Growth ◽  
Carbon Mineralization ◽  
Fungal Growth ◽  
Functional Redundancy ◽  
Ph Gradient ◽  
Total Carbon ◽  
Ph Effects ◽  
Acetate Incorporation ◽  
Growth Ratio

ABSTRACT The influence of pH on the relative importance of the two principal decomposer groups in soil, fungi and bacteria, was investigated along a continuous soil pH gradient at Hoosfield acid strip at Rothamsted Research in the United Kingdom. This experimental location provides a uniform pH gradient, ranging from pH 8.3 to 4.0, within 180 m in a silty loam soil on which barley has been continuously grown for more than 100 years. We estimated the importance of fungi and bacteria directly by measuring acetate incorporation into ergosterol to measure fungal growth and leucine and thymidine incorporation to measure bacterial growth. The growth-based measurements revealed a fivefold decrease in bacterial growth and a fivefold increase in fungal growth with lower pH. This resulted in an approximately 30-fold increase in fungal importance, as indicated by the fungal growth/bacterial growth ratio, from pH 8.3 to pH 4.5. In contrast, corresponding effects on biomass markers for fungi (ergosterol and phospholipid fatty acid [PLFA] 18:2ω6,9) and bacteria (bacterial PLFAs) showed only a two- to threefold difference in fungal importance in the same pH interval. The shift in fungal and bacterial importance along the pH gradient decreased the total carbon mineralization, measured as basal respiration, by only about one-third, possibly suggesting functional redundancy. Below pH 4.5 there was universal inhibition of all microbial variables, probably derived from increased inhibitory effects due to release of free aluminum or decreasing plant productivity. To investigate decomposer group importance, growth measurements provided significantly increased sensitivity compared with biomass-based measurements.

Do fungi and bacteria respond similar across a steep local pH gradient?

2021 ◽  
Author(s):  
Rasmus Kjoller ◽  
Carla Cruz-Paredes
Keyword(s):  
Community Composition ◽  
Soil Ph ◽  
Wood Ash ◽  
Ph Gradient ◽  
Fungal Communities ◽  
Ph Effects ◽  
Fungal Community Composition ◽  
Ph Gradients ◽  
Field Samples ◽  
Bacterial Richness

<p>Soil pH is consistently recorded as the single most important variable explaining bacterial richness and community composition locally as globally. Bacterial richness responds to soil pH in a bell-shaped pattern, highest in soils with near-neutral pH, while lower diversity is found in soil with pH >8 and <4.5. Also, community turnover is strongly determined by pH for bacteria. In contrast, pH effects on fungi is apparently less pronounced though also much less studied compared to bacteria. Still, pH appears to be a significant determinant for fungal communities but typically not the most important. Rarely are bacterial and fungal communities co-analyzed from the same field samples taken across pH gradients. Here we analyze the community responses of fungi and bacteria in parallel over an extreme pH gradient ranging from pH 4 to 8 established by applying strongly alkaline wood ash to replicated plots in a Picea abies plantation. Bacterial and fungal community composition were assessed by amplicon-based meta-barcoding. Bacterial richness were not significantly affected by pH, while fungal richness and a-diversity were stimulated with higher pH. We found that both, bacterial and fungal communities increasingly deviated from the untreated plots with increasing amount of wood ash though fungal communities were more resistant to changes than bacterial. Soil NH<sub>4</sub>, NO<sub>3</sub> and pH significantly correlated with the NMDS pattern for both bacterial and fungal communities. In the presentation we will discuss resistance versus sensitivity of different fungal functional guilds towards higher pH as well as the underlying factors explaining the community changes.</p>

Soil microbial growth and carbon-use efficiency: ecological control mechanisms

2020 ◽  
Author(s):  
Johannes Rousk
Keyword(s):  
Heavy Metal ◽  
Soil Ph ◽  
Bacterial Growth ◽  
Fungal Growth ◽  
Plant Litter ◽  
N Availability ◽  
Mineral N ◽  
Soil C ◽  
Carbon Use Efficiency ◽  
Use Efficiency

<p>During the decomposition of organic matter (OM), microorganisms use the assimilated carbon (C) for biomass production or respiration, and the fraction of growth to total assimilation defines the microbial carbon-use efficiency (CUE). Therefore, microbial CUEs have direct consequences for the balance of C between atmosphere and soil, and is as such a central parameter to represent the global C cycle well in Global Cycling Models (GCMs). Despite its enormous leverage this factor remains critically underexplored. Based on the physiology of cultured microorganisms, it is anticipated that (H1) high nutrient availabilities will increase microbial CUE, (H2) that higher quality substrate will increase microbial CUE, (H3) that microbial communities more dominated by fungi will have higher CUE, and (H4) that microbial CUE will decrease in response to environmental stress. We combined extensive field surveys with experimental treatments in microcosms to assess our hypotheses. We sampled temperate forest soils, temperate agricultural soils, and subarctic forest soils, encompassing a wide range of soil pHs (4.0-7.1), nutrient availabilities (10<soil C/N<33), and soil OM qualities (7-fold differences in respiration per SOM). We also surveyed environmental pollution gradients where metallurgy had contaminated soil with high heavy metal concentrations in boreal forest and temperate grassland sites. We also subjected selected soils to microcosm experiments where soil pH (liming), mineral N (50 kg N ha<sup>-1</sup>), OM quality (plant litter), or heavy metal stress were manipulated and the resulting bacterial and fungal growth, respiration, and CUE were monitored over the course of 2 months.</p><p> </p><p>Fungal-to-bacterial growth ratios (F:B) ranged from 0.02 to 0.44 across the studied ecosystems, and that the fungal dominance was higher in soils with lower C:N ratio and higher C-quality. CUE ranged from 0.03 to 0.30, and values clustered most strongly according to site rather than level of soil N. CUE was higher in soil with high C:N ratios and high C-qualities. However, within each land-use type, a high mineral N-content did result in lower F:B and higher resulting CUE. In the microcosm experiments, plant litter addition stimulated the growth of fungi more than bacteria, while increasing soil pH stimulated bacteria more than fungi. Mineral N additions inhibited bacterial growth and stimulated fungal growth. This resulted in microbial CUE estimates in real time that ranged from ca 0.05 to 0.55, and where increased pH and litter increased values while mineral N supplements decreased values. Long-term exposure to heavy metals decreased microbial CUE, but only marginally, even at very high rates of metal exposure. Short-term exposure to metal stimulated microbial CUE in soil from contaminated sites, while CUE was reduced in soil with no history of metal contamination. In conclusion, a higher site soil C-quality coincided with lower F:B and higher CUE across the surveyed sites, while a higher N availability did not. A higher site N availability resulted in higher CUE and lower F:B within each site, while mineral N supplements in the microcosm induced the opposite response, suggesting that site-specific differences associated with fertility such as the effect of plant communities, overrode the influence of mineral N-availability.</p>

scholarly journals Archaeal Abundance across a pH Gradient in an Arable Soil and Its Relationship to Bacterial and Fungal Growth Rates

2012 ◽  
Vol 78 (16) ◽  
pp. 5906-5911 ◽  
Author(s):  
Per Bengtson ◽  
Anna E. Sterngren ◽  
Johannes Rousk
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Soil Ph ◽  
Fungal Growth ◽  
Ph Gradient ◽  
Gene Copy ◽  
Rrna Gene ◽  
Copy Numbers ◽  
Ph Range ◽  
Gene Copy Numbers

ABSTRACTSoil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient.

scholarly journals Modeling biogeochemical processes in sediments from the Rhône River prodelta area (NW Mediterranean Sea)

2011 ◽  
Vol 8 (1) ◽  
pp. 549-592 ◽  
Author(s):  
L. Pastor ◽  
C. Cathalot ◽  
B. Deflandre ◽  
E. Viollier ◽  
K. Soetaert ◽  
...  
Keyword(s):  
Organic Matter ◽  
Oxygen Consumption ◽  
Continental Shelf ◽  
Carbon Mineralization ◽  
River Mouth ◽  
Total Carbon ◽  
Large Contribution ◽  
Organic Carbon Content ◽  
Rhône River ◽  
Rhone River

Abstract. In-situ oxygen microprofiles, sediment organic carbon content and pore-water concentrations of nitrate, ammonium, iron, manganese and sulfides obtained in sediments from the Rhône River prodelta and its adjacent continental shelf were used to constrain a numerical diagenetic model. Results showed that (1) organic matter from the Rhône River is composed of a fraction of fresh material associated to high first-order degradation rate constants (11–33 yr−1), (2) burial efficiency (burial/input ratio) in the Rhône prodelta (within 3 km of the river outlet) can be up to 80%, and decreases to ~20% on the adjacent continental shelf 10–15 km further offshore (3) there is a large contribution of anoxic processes to total mineralization in sediments near the river mouth, certainly due to large inputs of fresh organic material combined with high sedimentation rates, (4) diagenetic by-products originally produced during anoxic organic matter mineralization are almost entirely precipitated (>97%) and buried in the sediment, which leads to (5) a low contribution of the re-oxidation of reduced products to total oxygen consumption. Consequently, total carbon mineralization rates as based on oxygen consumption rates and using Redfield stoichiometry can be largely underestimated in such River Ocean dominated Margins (RiOMar) environments.

Soil pH effects on the toxicity of zinc oxide nanoparticles to soil microbial community

2018 ◽  
Vol 25 (28) ◽  
pp. 28140-28152 ◽  
Author(s):  
Concepción García-Gómez ◽  
María Dolores Fernández ◽  
Sandra García ◽  
Ana Francisca Obrador ◽  
Marta Letón ◽  
...  
Keyword(s):  
Zinc Oxide ◽  
Microbial Community ◽  
Soil Ph ◽  
Soil Microbial Community ◽  
Zinc Oxide Nanoparticles ◽  
Oxide Nanoparticles ◽  
Ph Effects ◽  
Soil Microbial

scholarly journals Effect of soil erosion and topography on distribution of cadmium (Cd) in Sumani watershed, west Sumatra, Indonesia

2018 ◽  
Vol 229 ◽  
pp. 03001 ◽  
Author(s):  
Aflizar ◽  
Aprisal ◽  
Cornelius Idowu Alarima ◽  
Tsugiyuki Masunaga
Keyword(s):  
Soil Erosion ◽  
Soil Ph ◽  
Volcanic Ash ◽  
River Sediments ◽  
Soil Survey ◽  
Total Carbon ◽  
High Soil ◽  
West Sumatra ◽  
Material Translocation ◽  
Carbon Erosion

The purpose of this study was to characterize and present the distribution of heavy metals especially Cd on agricultural and non-agricultural lands and river sediments in relation to soil erosion and topography status in watersheds. The study was conducted for a detailed soil survey by collecting 146 soil sample based on land use, soil family and topography position and 23 river sediments sample. The Cd was extracted by 0.1 M HCl and determined by ICP. The result showed that the concentration of Cd in soil and river sediment were low in toxicity based on FAO recommendation (Cd 0.4 mg/kg) with only 4 out of 169 sampling sites contained Cd exceeding the toxicity level. Volcanic ash from Mount Talang Volcano is a natural source of Cd in Sumani watershed. Cd concentration was low in areas with high soil erosion, which indicate material translocation caused by high soil erosion that accumulates sediment in plains and rivers. Agricultural soil was found to be low in soil pH and clay accompanied by high R factor and upland topography hence the increase in Cd concentration of the soil. The study concluded that Cd abundance in soils may be influenced by soil pH, texture, total carbon, erosion factors, and topography.

scholarly journals Linking Microbial Community Structure to Trait Distributions and Functions Using Salinity as an Environmental Filter

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Kristin M. Rath ◽  
Arpita Maheshwari ◽  
Johannes Rousk
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Salt Tolerance ◽  
Microbial Communities ◽  
Bacterial Growth ◽  
Soil Microbes ◽  
Fungal Growth ◽  
Environmental Filter ◽  
Trait Distribution ◽  
Nonsaline Soil

ABSTRACT The structure and function of microbial communities vary along environmental gradients; however, interlinking the two has been challenging. In this study, salinity was used as an environmental filter to study how it could shape trait distributions, community structures, and the resulting functions of soil microbes. The environmental filter was applied by salinizing nonsaline soil (0 to 22 mg NaCl g−1). Our targeted community trait distribution (salt tolerance) was determined with dose-response relationships between bacterial growth and salinity. The bacterial community structure responses were resolved with Illumina 16S rRNA gene amplicon sequencing, and the microbial functions determined were respiration and bacterial and fungal growth. Salt exposure quickly resulted in filtered trait distributions, and stronger filters resulted in larger shifts. The filtered trait distributions correlated well with community composition differences, suggesting that trait distribution shifts were driven at least partly by species turnover. While salt exposure decreased respiration, microbial growth responses appeared to be characterized by competitive interactions. Fungal growth was highest when bacterial growth was inhibited by the highest salinity, and it was lowest when the bacterial growth rate peaked at intermediate salt levels. These findings corroborated a higher potential for fungal salt tolerance than bacterial salt tolerance for communities derived from a nonsaline soil. In conclusion, by using salt as an environmental filter, we could interlink the targeted trait distribution with both the community structure and resulting functions of soil microbes. IMPORTANCE Understanding the role of ecological communities in maintaining multiple ecosystem processes is a central challenge in ecology. Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial processes to community composition and structure. Here, we apply a conceptual framework to determine how microbial communities influence ecosystem processes, by applying a “top-down” trait-based approach. By determining the dependence of microbial processes on environmental factors (e.g., the tolerance to salinity), we can define the aggregate response trait distribution of the community, which then can be linked to the community structure and the resulting function performed by the microbial community.

Evaluation of Bacterial and Fungal Growth Media for Ability to Neutralize Cosmetic Preservatives

1980 ◽  
Vol 63 (6) ◽  
pp. 1200-1204
Author(s):  
Allan M Littell ◽  
Michael J Palmieri ◽  
Neil B Bisciello
Keyword(s):  
Bacterial Growth ◽  
Fungal Growth ◽  
Tween 80 ◽  
Fungal Species ◽  
Growth Media ◽  
Malt Extract ◽  
Bacterial Strains ◽  
Standard Methods ◽  
Bacterial Cultures ◽  
Plate Counts

Abstract Standard methods agar (SMA) and letheen agar (essentially SMA plus lecithin and Tween 80) were compared for bacterial growth and ability to neutralize cosmetic preservatives. Potato dextrose and malt extract agars (each prepared with and without lecithin and Tween 80) were compared with letheen agar and SMA in similar studies with fungi. Twelve bacterial strains, representing 8 species, and 2 fungal species were used as inocula. Plate counts of bacterial cultures (no preservatives present) ranged from 0 to 50% higher on letheen agar than on SMA except for 3 strains of Staphylococcus, which were 8-29% lower. Fungal counts were about the same on all media. Cosmetics (10 g) representing 4 preservative systems (hexachlorophene, benzoin, formaldehyde, and parabens) were inoculated with diluted cultures. Counts at 10−1 and 10−2 dilutions were typically 10-200% higher on letheen agar; however, in one case (benzoin, S. aureus, 10−1) the count was 400 on SMA vs 20 000 on letheen agar. Although differences in fungal counts were not as great, letheen agar partially neutralized the preservatives’ action. Results show that product dilution does not sufficiently reduce the effects of preservative carryover and neutralizers should be incorporated into plating media for this purpose.

The influence of nutrients on fungal growth, productivity, and sporulation during leaf breakdown in streams

1995 ◽  
Vol 73 (S1) ◽  
pp. 1361-1369 ◽  
Author(s):  
Keller Suberkropp
Keyword(s):  
Growth Rates ◽  
Fungal Biomass ◽  
Fungal Growth ◽  
Aquatic Hyphomycetes ◽  
Acetate Incorporation ◽  
Yellow Poplar ◽  
Leaf Breakdown ◽  
Leaf Surfaces ◽  
Good Agreement ◽  
Growth And Reproduction

In streams, aquatic hyphomycetes degrade leaf litter and transform it into a more suitable resource for invertebrate detritivores. Previous studies have demonstrated that fungi comprise a major portion of the microbial biomass associated with decomposing leaves and that inputs of leaves in the autumn reduce the concentration of soluble phosphorus in the water. These observations indicate that fungi obtain inorganic nutrients from the water passing over leaf surfaces. However, very little is known concerning the effects of nutrients on the activity of the fungi growing within leaves. To examine this question, I determined fungal biomass (from ergosterol concentrations) and sporulation rates during the breakdown of yellow poplar (Liriodendron tulipifera) leaves in three streams that differed in water chemistry. I also estimated instantaneous growth rates by measuring rates of [14C]acetate incorporation into ergosterol and calculated fungal productivity from growth rates and biomass. Growth rates and productivity determined by this method showed good agreement with values calculated from changes in fungal biomass during early stages of leaf breakdown for two of the streams examined. Highest concentrations of fungal biomass and greatest fungal activity occurred in the stream with the highest concentrations of nutrients. However, differences in total fungal production and biomass were not as great as were differences among sporulation rates in the three streams suggesting that fungal allocation of resources to growth and reproduction can vary depending on nutrient availability. Key words: aquatic hyphomycetes, ergosterol, leaf breakdown, nutrients, fungal productivity, streams.

INHIBITION OF FUNGAL GROWTH BY BACTERIA DURING CELLULOSE-DECOMPOSITION

1961 ◽  
Vol 7 (6) ◽  
pp. 857-863 ◽  
Author(s):  
Y. Henis ◽  
Paulina Keller ◽  
A. Keynan
Keyword(s):  
Bacterial Growth ◽  
Filter Paper ◽  
Vegetative Growth ◽  
Pure Culture ◽  
Carboxymethyl Cellulose ◽  
Agar Medium ◽  
Fungal Growth ◽  
Fungal Development ◽  
Cellulose Decomposition ◽  
Cellulose Filter

The cellulose-decomposing flora developing from soil crumbs on filter paper placed upon an agar medium was studied. Under these conditions fungal development was significantly inhibited by bacterial growth. When cellophane was substituted for filter paper, no inhibition of fungal growth was observed. A pure culture of Cellvibrio inhibited the vegetative growth of Stachybotrys when inoculated simultaneously on media containing carboxymethyl-cellulose, filter paper, or glucose up to 0.1%. This inhibition was shown to be caused by competition for available carbohydrates.

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