Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

Agricultural land management, such as fertilization, liming, and tillage affects soil properties, including pH, organic matter content, nitrification rates, and the microbial community. Three different study sites were used to identify microorganisms that correlate with agricultural land use and to determine which factors regulate the relative abundance of the microbial signatures of the agricultural land-use. The three sites included in this study are the Broadbalk Experiment at Rothamsted Research, UK, the Everglades Agricultural Area, Florida, USA, and the Kellogg Biological Station, Michigan, USA. The effects of agricultural management on the abundance and diversity of bacteria and archaea were determined using high throughput, barcoded 16S rRNA sequencing. In addition, the relative abundance of these organisms was correlated with soil features. Two groups of microorganisms involved in nitrogen cycle were highly correlated with land use at all three sites. The ammonia oxidizing-archaea, dominated by Ca. Nitrososphaera, were positively correlated with agriculture while a ubiquitous group of soil bacteria closely related to the diazotrophic symbiont, Bradyrhizobium, was negatively correlated with agricultural management. Analysis of successional plots showed that the abundance of ammonia oxidizing-archaea declined and the abundance of bradyrhizobia increased with time away from agriculture. This observation suggests that the effect of agriculture on the relative abundance of these genera is reversible. Soil pH and NH(3) concentrations were positively correlated with archaeal abundance but negatively correlated with the abundance of Bradyrhizobium. The high correlations of Ca. Nitrososphaera and Bradyrhizobium abundances with agricultural management at three long-term experiments with different edaphoclimatic conditions allowed us to suggest these two genera as signature microorganisms for agricultural land use

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

Agricultural land management, such as fertilization, liming, and tillage affects soil properties, including pH, organic matter content, nitrification rates, and the microbial community. Three different study sites were used to identify microorganisms that correlate with agricultural land use and to determine which factors regulate the relative abundance of the microbial signatures of the agricultural land-use. The three sites included in this study are the Broadbalk Experiment at Rothamsted Research, UK, the Everglades Agricultural Area, Florida, USA, and the Kellogg Biological Station, Michigan, USA. The effects of agricultural management on the abundance and diversity of bacteria and archaea were determined using high throughput, barcoded 16S rRNA sequencing. In addition, the relative abundance of these organisms was correlated with soil features. Two groups of microorganisms involved in nitrogen cycle were highly correlated with land use at all three sites. The ammonia oxidizing-archaea, dominated by Ca. Nitrososphaera, were positively correlated with agriculture while a ubiquitous group of soil bacteria closely related to the diazotrophic symbiont, Bradyrhizobium, was negatively correlated with agricultural management. Analysis of successional plots showed that the abundance of ammonia oxidizing-archaea declined and the abundance of bradyrhizobia increased with time away from agriculture. This observation suggests that the effect of agriculture on the relative abundance of these genera is reversible. Soil pH and NH₃ concentrations were positively correlated with archaeal abundance but negatively correlated with the abundance of Bradyrhizobium. The high correlations of Ca. Nitrososphaera and Bradyrhizobium abundances with agricultural management at three long-term experiments with different edaphoclimatic conditions allowed us to suggest these two genera as signature microorganisms for agricultural land use.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at: http://www.frontiersin.org/Microbiology.Keywords: Ca. Nitrososphaera, Agricultural land use, Bradyrhizobium, Ammonia-oxidizing archaea, Soil properties, DiazotrophsKeywords: Ca. Nitrososphaera, Agricultural land use, Bradyrhizobium, Ammonia-oxidizing archaea, Soil properties, Diazotroph

Growth Efficacy of Sorghum and Rice Amended with Dried Versus Composted Aquatic Vegetation

Aquatic vegetation is a potential source of organic matter and nutrients for crop production and soil sustainability. However, its high water content and presence of toxic compounds have been major deterrents for commercial application. This split-pot study evaluated the application of Pistia stratiotes (PS) (water lettuce) and Lyngbya wollei (LW) (filamentous cyanobacteria) to grow rice and sorghum. The aquatic vegetation was applied as dried and composted amendments on sandy (80% organic matter) soils. A completely randomized split-pot design evaluated the effect of the amendments on root dry weight (RDW), shoot dry weight (SDW), and nutrient content of above ground biomass. The application of dried PS and LW on sandy soil produced larger and heavier sorghum shoots than those grown under composted treatments. Soil type was not a determinant factor of plant nutrient content: total Kjeldahl nitrogen, phosphorus, potassium and silicon. Shoot dry weight of rice grown on sandy soils was significantly greater than grown on muck soils using dried LW and composted LW treatments. The allelopathic effects of PS and LW were more pronounced on sandy soil compared to muck soil, indicating the potential application for using aquatic vegetation as a soil amendment on sandy soil in the future

Allelopathic Effects of Pistia stratiotes (Araceae) and Lyngbya wollei Farlow ex Gomont (Oscillariaceae) on Seed Germination and Root Growth

Pistia stratiotes and Lyngbya wollei are the two most common aquatic weeds that flourish in farm canals within the Everglades Agricultural Area of Florida. Identifying a useful application of these weeds would not only address important environmental concerns, but would also be an incentive for farmers to harvest it. The objective of this study was to determine use of P. stratiotes and L. wollei as soil amendments for stimulation of seed germination and root growth in different plant species. The effects of different rates of dried and grounded P. stratiotes and L. wollei on germination and root length of snap bean, corn, sorghum, common lambsquarters, and rice were evaluated using a controlled petri-dish incubation bioassay study. Overall, both amendments had a negative allelopathic effect on germination of all species. The highest reduction in germination of 80 and 43% by P. stratiotes and L. wollei respectively was observed on corn. Rice was the most tolerant to allelopathic effects that emanated from both amendments. There was a significant positive increase in rice root length in response to P. stratiotes rate over the two-week period. This study shows that P. stratiotes can be used as a potential bio-fertilizer to stimulate early growth of rice

Ontology-based simulation of water flow in organic soils applied to Florida sugarcane

An ontology-based simulation (OntoSim) is a unique data modeling environment where soil-plant-nutrient processes are represented as database objects and the user-defined relationships among objects are used to generate computer code (Java) for running the simulation. The aim of this study was to model hydrologic processes of sugarcane-grown organic soils utilizing OntoSim in the Everglades Agricultural Area (EAA) of South Florida. This OntoSim-Sugarcane model describes the complex hydrology of sub-irrigation and open ditch drainage commonly used on Florida farms. Model calibration was conducted by (i) selecting rectangular farm water management units ( 0.65; coefficient of residual mass 0.55 and coefficient of residual massOntology Simulation Hydrology Everglades Agricultural Area Water table Drainage

Comparison of protein coding sequences (CDS) of <i>Ca</i>. Nitrososphaera evergladensis with CDS of other ammonia-oxidizing archaea.

<p>(A) CDS of <i>Ca</i>. Nitrososphaera evergladensis were compared to CDS of <i>Ca</i>. N. gargensis. (B) CDS of the group I.1a (<i>N. maritimus</i>, <i>Ca</i>. N. sediminis, <i>C. symbiosum</i>, <i>Ca</i>. N. limnia, <i>Ca</i>. N. koreensis) were compared to CDS of the group I.1b (<i>Ca</i>. N. evergladensis and <i>Ca</i>. N. gargensis). Overlapping regions represent CDS with amino acid sequence identity 35% and higher.</p

Organization of (A) urease and urea transporter genes; (B) ammonia monooxygenase gene order of <i>Ca</i>. N. evergladensis; (C) flagella and chemotaxis genes in the present genome.

<p>Organization of (A) urease and urea transporter genes; (B) ammonia monooxygenase gene order of <i>Ca</i>. N. evergladensis; (C) flagella and chemotaxis genes in the present genome.</p

Components of the nitrogen metabolism of <i>Ca</i>. N. evergladensis

<p>: ammonia oxidation (4, 5), ammonia assimilation (8, 9, 10), nitrite reduction (6), nitrous oxide production (7). Reactions are mediated by the following transporters and enzymes: urea transporters, urease (1, 2), ammonia transporters (3), archaeal ammonia monooxygenase (AMO) (4), candidate enzyme: multicopper oxidase (5), nitrite reductase (NirK) (6), nitric oxide reductase (NorD, NorQ), catalytic subunit (NorB) is missing (7), glutamate dehydrogenase (8), glutamine synthetase (9), glutamate synthase (10). NO may upregulate activity of AMO. * - experimental evidences are needed.</p