Thursday, April 28, 2011

Organic and Conventional Farming Compared on Weeds

The quick answer is that there is little difference that can be safely ascertained and that there is no reason to alter practice of the account of it.  More detailed analysis may tell us something different but I suspect that any such information would indicate additional effort also.

At least someone asked the question and it looks as something that is safe to ignore as an issue.

Organic and Conventional Farming Methods Compete to Eliminate Weed Seeds in Soil

Released: 4/21/2011 9:00 AM EDT 

Newswise — Weeds are hard to kill; they seem to come back no matter what steps people take to eradicate them. One reason is because of the persistence of weed seeds in the soil. Organic farming and conventional farming systems both have their methods of taking on weed seeds, but does one show better results than the other?

The authors of a study reported in the current issue of the journal Weed Science conducted tests that compared conventional farming with organic systems. This research determined weed seed viability under both systems over a two-year period in two separate locations.

To compare these systems, researchers buried seeds of two types of weeds, smooth pigweed and common lambsquarters, in mesh bags. Tests were conducted at agricultural research locations in Maryland and Pennsylvania. Seed viability was determined by retrieving seeds every six months over the two-year period.

Depth of seeds in the soil, environmental conditions, and soil management are among the factors that affect seed persistence. Under conventional soil management, tillage is an important practice that manipulates the depth of seeds and environmental conditions that can influence weed seed persistence. Organic soils have enhanced biological activity, with more carbon, moisture, and microbial activity that could lead to greater seed decomposition.

The organic soils in this study were higher in total soil microbial biomass than the soils of the conventional farming tests. This was measured by phospholipid fatty acid content. But the results of the tests did not lead researchers to conclude that this microbial biomass has a dominating role in seed mortality.

Pigweed seeds showed a shorter life span under the organic system in two of four experiments. Organic system lambsquarters seeds had a shorter life span in just one of the four experiments, while the conventional methods had the shorter life span in two of four experiments. These results leave an ambiguous answer to the question of which farming system can better eliminate seeds deep in the soil to control weeds from their source.

About Weed Science

Weed Science is a journal of the Weed Science Society of America, a non-profit professional society that promotes research, education, and extension outreach activities related to weeds; provides science-based information to the public and policy makers; and fosters awareness of weeds and their impacts on managed and natural ecosystems. For more information, visit


Weed Seed Persistence and Microbial Abundance in Long-Term Organic and Conventional Cropping Systems

Silke D. Ullrich, Jeffrey S. Buyer, Michel A. Cavigelli, Rita Seidel, and John R. Teasdale*

Weed seed persistence in soil can be influenced by many factors, including crop management. This research was conducted to determine whether organic management systems with higher organic amendments and soil microbial biomass could reduce weed seed persistence compared with conventional management systems. Seeds of smooth pigweed and common lambsquarters were buried in mesh bags in organic and conventional systems of two long-term experiments, the Farming Systems Project at the Beltsville Agricultural Research Center, Maryland, and the Farming Systems Trial at the Rodale Institute, Pennsylvania. Seed viability was determined after retrieval at half-year intervals for 2 yr. Total soil microbial biomass, as measured by phospholipid fatty acid (PLFA) content, was higher in organic systems than in conventional systems at both locations. Over all systems, locations, and experiments, viable seed half-life was relatively consistent with a mean of 1.3 and 1.1 yr and a standard deviation of 0.5 and 0.3 for smooth pigweed and common lambsquarters, respectively. Differences between systems were small and relatively inconsistent. Half-life of smooth pigweed seeds was shorter in the organic than in the conventional system in two of four location-experiments. Half-life of common lambsquarters was shorter in the organic than in the conventional system in one of four location-experiments, but longer in the organic than in the conventional system in two of four location-experiments. There were few correlations between PLFA biomarkers and seed half-lives in three of four location-experiments; however, there were negative correlations up to −0.64 for common lambsquarters and −0.55 for smooth pigweed in the second Rodale experiment. The lack of consistent system effects on seed persistence and the lack of consistent associations between soil microbial biomass and weed seed persistence suggest that soil microorganisms do not have a dominating role in seed mortality. More precise research targeted to identifying specific microbial functions causing seed mortality will be needed to provide a clearer picture of the role of soil microbes in weed seed persistence.
Nomenclature: Common lambsquarters, Chenopodium album L. CHEAL; smooth pigweed, Amaranthus hybridus L. AMACH
Received: September 29, 2010; Accepted: January 10, 2011
*First, second, third, and fifth authors: Research Associate, Chemist, Soil Scientist, and Plant Physiologist, U.S. Department of Agriculture-Agricultural Research Service Sustainable Agricultural Systems Lab, Beltsville, MD 20705; fourth author: Agroecologist, Rodale Institute, Kutztown, PA 19530. Corresponding author's E-mail: 

Persistence of weed seeds in soil is critical to the survival of annual weeds in agroecosystems. Seed mortality is a demographic process that can have a major impact on presence and dynamics of weed populations (Cousens and Mortimer 1995; Mohler 2001). Many factors have been shown to affect weed seed persistence including species (Buhler and Hartzler 2001), maternal environment (Schutte et al. 2008), depth in soil (Conn et al. 2006), environmental conditions (Davis et al. 2005), and soil management (Davis et al. 2006; Fennimore and Jackson 2003; Lutman et al. 2002; Steckel et al. 2007). Understanding soil management effects on seed persistence is particularly important because it offers producers the opportunity to manage weed seed populations through cultural practices. Tillage is an important operation that can allow manipulation of seed depth and associated environmental conditions that influence seed persistence (Lutman et al. 2002; Steckel et al. 2007). Amending the soil with organic inputs in reduced input or organic farming systems also can influence seed persistence and weed seedbank levels (Davis 2007; Davis et al. 2006; Fennimore and Jackson 2003; Gallandt et al. 1998).

Several approaches have been used to assess the persistence of seeds in soil, ranging from methods that maintain seed in a natural soil environment with less precision of recovery to methods that create an artificial soil environment but increase precision of recovery. An example of the former approach is to begin an experiment with a high natural population (Schweizer and Zimdahl 1984; Steckel et al. 2007) or to pulse with a defined initial density of seeds that may be subject to experimental management practices (Buhler and Hartzler 2001; Lutman et al. 2002) followed by subsequent soil sampling. More precise recovery of the initial seed lot can be achieved by installation of seeds in unenclosed soil cylinders that can be subsequently recovered in their entirety (Schutte et al. 2008; Teo-Sherrell et al. 1996). Mesh bags or other porous seed enclosures provide an artificial barrier to the surrounding soil, and permit high recovery precision of the initial seed lot (Conn et al. 2006; Davis et al. 2005; Gallandt et al. 2004). Schutte et al. (2008) found the mesh bag and core methods resulted in similar seed persistence and mortality, althoughVan Mourik et al. (2005) warn that high seed-to-soil ratios in mesh bags can lead to excessive fungus-induced mortality.

Gallandt et al. (1999) suggested that enhanced soil biological activity resulting from improved soil quality could increase the mortality of weed seeds in soil. Kennedy (1999)proposed that no-tillage and biologically based systems that enhance soil carbon, moisture, and microbial activity may predispose these systems to greater seed decomposition. Soil managed for high organic matter and reduced tillage had soil quality indicators, enzyme activity, and water stable aggregates that were associated with weed-suppressive bacterial isolates (Kremer and Li 2003). However, the major causes of seed mortality include not only microbe-induced decay, but also fatal germination, physiological aging, and predation (Gallandt et al. 2004). Losses from predation can be distinguished from the other mortality factors by confining seed in containers that exclude the predator in question. It is often difficult to distinguish among microbial decay, aging, and fatal germination in container experiments. Fatal germination can occur when seed germination is induced under conditions that do not permit successful emergence (Benvenuti et al. 2001; Gallandt et al. 2004). Research oriented to crop seed preservation has shown that glassification of seed sugars can protect seed from destruction by various physiological aging mechanisms involving free-radical and enzymatic destruction of essential cell molecular components (Bernal-Lugo and Leopold 1998). Thus, microbial destruction of the seed coat could lead not only to microbial decay of seeds but also to moisture conditions that would induce a phase shift in glassification and acceleration of physiological aging processes.

Long-term systems experiments with a range of cropping systems that differ in soil organic inputs offer an opportunity to investigate the potential impact of enhanced soil microbial activity on weed seed persistence (Davis et al. 2006; Gallandt et al. 2004; Kremer and Li 2003). The Rodale Institute Farming Systems Trial (FST) near Kutztown, PA, was initiated in 1981 and is the longest running comparison of conventional and organic cropping systems in the United States. Soil carbon and nitrogen became significantly greater in the organic compared to the conventional system over the first 22 yr of this experiment (Pimentel et al. 2005). The U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS) Farming Systems Project (FSP) at Beltsville, MD, was initiated in 1996 and also includes a comparison of conventional and organic cropping systems. The two most important weed species in the FSP organic systems are smooth pigweed and common lambsquarters, whose soil seed populations have been shown to fluctuate widely depending on annual seed inputs (Teasdale et al. 2004). Given the relative volatility of the seedbank of these species, we hypothesized that this may have been caused, in part, by increased mortality from soil amendments associated with organic systems in these long-term experiments.

The objective of this research was to compare the persistence of smooth pigweed and common lambsquarters in the FSP and FST organic and conventional cropping systems within mesh bags that eliminated mortality effects of predators. Our hypothesis was that increased soil microbial biomass in organic systems are associated with shorter seed persistence. Since soil depth can influence the environmental conditions and microbial activity that seeds encounter, a second objective was to compare seed persistence at two seed depths, 5 and 15 cm.

Materials and Methods

Experimental Site Description.

Seed persistence experiments were conducted at two long-term experimental sites: FSP, begun in 1996 and located at the Beltsville Agricultural Research Center (BARC), Maryland, and FST, begun in 1981 and located at the Rodale Institute near Kutztown, PA. Experiments reported here were conducted during the first decade of the FSP and during the third decade of the FST.

At BARC, experiments were conducted in two of the five FSP cropping systems, a conventional chisel-tillage system and an organic system. These systems were chosen because they followed a similar 3-yr corn (Zea mays L.)–soybean [Glycine max (L.) Merr.]–wheat (Triticum aestivum L.) rotation, so that confounding effects of rotation would be minimized. Detailed description of the systems and crop performance during the first 10 yr of this cropping systems experiment are outlined in Cavigelli et al. (2008). In brief, the conventional system was farmed using locally recommended fertilizer and herbicide programs. The organic system relied on cover crops (hairy vetch [Vicia villosa Roth] before corn and rye [Secale cereale L.] before soybean] plus poultry litter for providing and/or retaining nutrients, and on rotary hoeing and sweep cultivation for weed control. Both the conventional and the organic systems included plowing and disking for seedbed preparation.

At Rodale, experiments were conducted in two of three FST cropping systems, a conventional and an organic system. A corn–corn–soybean–corn–soybean rotation was followed in the conventional system with recommended fertilizer and herbicide inputs. The legume-based organic system at FST was chosen because it followed a corn–soybean–wheat rotation similar to that used in the FSP 3-yr organic system. This organic system relied on various legume cover crops for providing nitrogen to grain crops, on a rye cover crop for retaining nutrients following corn, and on rotary hoeing and sweep cultivation for weed control. Both the conventional and the organic systems included plowing and disking for seedbed preparation. One exception to cropping patterns occurred in 2003, when oats (Avena sativa L.) were planted as a uniformity crop over the entire trial. Further details on FST cropping systems management and system performance can be obtained in Pimentel et al. (2005).

Seed and Soil Handling.

Smooth pigweed and common lambsquarters seeds that had been collected at BARC were placed in flat, square nylon bags with 6.75 cm interior length per side and a mesh size of 0.5 mm. Seed viability was initially tested by germination followed by a forceps squeeze test of ungerminated seeds. Each bag was filled with 200 viable seeds of a species along with 72 cm3 of field soil, which was obtained from the targeted burial location and system and dry sieved to eliminate resident weed seed. Bags were installed in a horizontal position in plots at 5- or 15-cm depths, avoiding wheel track areas. Bags were installed at two locations per plot and in four blocks per cropping system per location.

In order to eliminate crop effects, bags were only put in soil during the soybean phase of each rotation. Bags were installed in plots in the fall after harvest of the previous corn crop and planting of a rye cover crop (late October to early November). Four sets of bags were installed, with each set to be retrieved at half-year intervals over a 2-yr period. Bags were retrieved in the spring before field preparation for soybean planting (late April to early May). The set designated for removal in the first spring was taken to the lab for testing while the remaining sets were temporarily placed in soil near the edge of adjacent plots within the same cropping system while the experimental plots were prepared for planting. After soybean planting, sets designated for later retrieval were replaced into their designated plots at their designated depths beneath the soybean row to avoid damage by subsequent between-row cultivations. Bags were again retrieved in the fall after soybean harvest. The set designated for removal in the first fall was taken to the lab and the remaining sets were moved to plots planted to rye and destined for soybeans in the next season. A similar process was repeated to exhume the sets designated for spring and fall removal during the second season. The first experiment consisted of four sets of bags that were initially installed in the fall of 2001 and removal was completed in the fall of 2003. A second experiment consisted of an additional four sets of bags that were initially installed in the fall of 2002 and removal was completed in the fall of 2004.

In the lab, bags were washed clean of soil with tap water and blotted dry. Bags were dipped in 70% ethanol for 30 s, rinsed with deionized water, dipped in 10% Clorox1 for 5 min, rinsed again with deionized water, and blotted dry with a paper towel. When bags were dry, seeds were transferred to petri dishes containing Whatman no. 3 filter paper and 7.5 ml deionized water. Dishes were sealed with parafilm and placed in a growth chamber at constant 30 C for smooth pigweed or 20 C for common lambsquarters. Germinated seeds were counted and removed from the dish after 1 wk. Plates were moistened as needed, resealed, and counted after another week. Remaining ungerminated seeds were squeezed with a forceps and identified as viable if the endosperm was white and firm (Sawma and Mohler 2002).

A composite of 10 soil samples was taken to 15-cm depth near each burial site in each plot for soil microbial biomass and community analysis. Samples were taken at three times during the season, in early April before spring tillage, in June after soybean planting, and in early October before soybean harvest. Soil was placed in a sealed plastic bag and transported in a cooler to the lab. Soil was sieved through a 0.6-cm screen and stored at −20 C. Phospholipid fatty acid analysis of soil microbial communities was conducted as previously described (Buyer et al. 2010). Biomarkers for gram-positive bacteria, gram-negative bacteria, actinomycetes, fungi, and protozoa were as described by Buyer et al. (2010). In addition, the sum of 15 0, 15  1 iso and anteiso, 17  0 cyclo, 17  0 iso, and 17  1 iso and anteiso was used as a biomarker for eubacteria (Frostegård and Bååth, 1996). The sum of polyunsaturated fatty acids was used as a biomarker for eukaryotes, and the total phospholipid fatty acid (PLFA) concentration was used as a biomarker for total microbial biomass (Zelles 1999).

Data Analysis.

The percentage of seed surviving at each exhumation date was computed by dividing the measured number of germinated plus viable ungerminated seeds by the initial number of viable seeds in each packet ( =  200). For each location and experiment, survival values from each block of each system were regressed onto time (unit  =  yr) using a log-logistic model with asymptotes at 100 and 0 (Schabenberger et al. 1999where b is a shape parameter and LT50 is an estimate of the lethal time for 50% seed mortality. Thus, eight data points representing four times of exhumation and two replications at each time were used to determine LT50 values for each of four blocks of each system. A four-way ANOVA was conducted to analyze LT50 values relative to location, system, experiment, and depth using a mixed model procedure (PROC MIXED, SAS version 9.1.32). Since the organic systems and conventional systems were similar at the two locations, these were coded as common systems (organic or conventional) across locations. Only three species–location–system–experiment–depth blocks from this factorial set of treatments failed to give a reliable LT50 estimate; these were treated as missing values for the analysis.
PLFA biomarkers were analyzed using ANOVA and MANOVA with the general linear model (PROC GLM). A one-way model was employed in which the main effect consisted of the four cropping systems across both locations with year and sampling time treated as replications. For MANOVA, biomarkers were first transformed as the square root of the proportional biomarker (Hellinger transformation; Legendre and Gallagher 2001) and then standardized to unit variance. A canonical variates analysis, generated by the MANOVA, was used to identify the linear combination of variables that best separated the cropping systems (Buyer et al. 1999; Seber 1984). Pearson coefficients were determined for the correlation between PLFA biomarkers and seed survival half-lives.

Results and Discussion

Seed Persistence.

The majority of seed buried in these experiments did not persist for 2 yr. Generally, most seed persisted through the first winter (mean survival at the first spring exhumation date was 87 and 83% for common lambsquarters and smooth pigweed, respectively), but then exhibited higher mortality in the first summer (mean survival at the first fall exhumation date was 49 and 61% for common lambsquarters and smooth pigweed, respectively). By the end of 2 yr, mean survival was 20 and 29% for common lambsquarters and smooth pigweed, respectively. Because this pattern resulted in a sigmoid-shaped response for most data sets, data were fit to a log-logistic function rather than to an exponential decay function, which is often employed for fitting seed persistence data (Conn et al. 2006;Lutman et al. 2002).

Analysis of half-life values demonstrated a location by experiment by system interaction for smooth pigweed (P  =  0.0945) and common lambsquarters (P  =  0.0048). Smooth pigweed seed half-life was shorter in organic than in conventional systems in the second experiment at both locations (Table 1). Common lambsquarters seed half-life also was shorter in organic than in conventional system in the second Rodale experiment, but was longer in organic than in conventional systems in both BARC experiments. Smooth pigweed and common lambsquarters survival was high in both systems at the first spring exhumation date, but survival differentials between systems usually became most pronounced at the first fall exhumation date. This survival pattern can be seen in the second BARC experiment in which system differences were particularly prominent for both species (Figure 1).

The inconsistent survival responses to system, location, and experiment can not be explained by weather. Seasonal air temperatures were relatively similar between years and locations, although temperatures at Rodale tended to be slightly, but consistently lower than those at BARC (Table 2). Rainfall also followed a similar pattern at the two locations, with rainfall at Rodale higher than that at BARC in all but one of the 6-mo periods. Rainfall differentials between Rodale and BARC were most pronounced during the summers of 2002 and 2004. This rainfall difference may have contributed to the lower smooth pigweed half-life at Rodale than BARC (1.0 vs. 1.6), but had no effect on the half-life of common lambsquarters (1.1 and 1.0 at Rodale and BARC, respectively). The difference between higher temperatures during summer burial period (18 to 21 C) and lower temperatures during the winter burial period (1 to 8 C) was the most consistent weather trend observed (Table 2). Higher mortality during the first summer than winter burial periods at both locations (Figure 1) was probably related to this temperature differential. Mortality mechanisms dependent on biochemical or metabolic reactions would be enhanced by higher temperatures.

Despite the differences among system half-lives observed, these differences were relatively small (months), and half-lives in both systems were short (less than 2 yr) in all location-experiments (Table 1). The seed persistence half-lives of approximately 1 to 2 yr reported here are similar to those reported by other researchers using a range of methodologies. Half-lives for Amaranthus species ranged from < 1 to 2 yr in experiments using natural seedbank decline (Schweizer and Zimdahl 1984), pulse seeding without containers (Buhler and Hartzler 2001), and mesh bags (Davis et al. 2005). Common lambsquarters half-lives ranged from 1 to 2.5 yr in experiments with natural seedbanks (Schweizer and Zimdahl 1984), pulse seeding (Lutman et al. 2002), and mesh bags (Conn et al. 2006; Davis et al. 2005). The relatively longer half-life of 2.5 yr was observed under relatively colder Alaskan conditions (Conn et al. 2006), which undoubtedly would have delayed decay or aging processes compared to those in warmer climates. A longer common lambsquarters half-life of 4.5 yr was observed at one location in a United Kingdom experiment (Lutman et al. 2002), but this data set was limited by an unusually low initial recovery value following pulse seeding that probably upwardly biased this half-life estimate. Common lambsquarters seemingly persisted for many years when buried in cylinders in Nebraska (Burnside et al. 1996), but it is difficult to compute a reliable half-life from their data because no assessments of viability or dormancy were made other than a germination test.

It is also clear that a minority of smooth pigweed and common lambsquarters seed can persist for many years. In all of the studies reported above, some viable seed were always present at the conclusion of the experiment, whether 4 to 6 yr (Buhler and Hartzler 2001;Schweizer and Zimdahl 1984; Steckel et al. 2007), 17 yr (Burnside et al. 1996), or 20 yr (Conn et al. 2006). This suggests that seed cohorts of these species are made up of both short-lived and long-lived seeds. The production of heterogeneous seed types with respect to dormancy, dispersion, and persistence is a strategy that ensures survival under potentially variable edaphic and environmental conditions (Matilla et al. 2005). Common lambsquarters is known to produce heteromorphic brown and black seeds that vary in seed coat thickness, dormancy, and stress tolerance (Yao et al. 2010). Future research on seed persistence probably requires a more thorough characterization of both the initial viability of seed lots as well as the proportions of distinct heteromorphic seed types.

Seed Depth.

There were few significant effects of seed burial depth on half-life. There was a location by depth interaction in which smooth pigweed half-life was shorter when buried at the 5-cm than at the 15-cm depth at BARC (1.35 vs. 1.95 yr, respectively), but there was no significant difference at Kutztown (1.0 vs. 0.9 yr, respectively). There was a location by experiment by system by depth interaction for common lambsquarters half-life, but this involved a significant difference in depth at only one of eight location–experiment–system levels while there were no significant differences at the other seven levels (data not shown).

Other research using mesh bag methodology has reported no effect amongst 0- to 10-cm (Davis et al. 2005) or 2- to 15-cm (Conn et al. 2006) depths on common lambsquarters persistence. Clearly, in the absence of seed enclosures, seed on the soil surface would be more prone to predation than those buried in the soil (Menalled et al. 2007; Mohler and Galford 1997; Navntoft et al. 2009); however, losses to mechanisms other than predation appear to have a more subtle relationship to depth. Fatal germination is a potential loss mechanism that could account for depth-dependent seed mortality. Common lambsquarters and redroot pigweed have been shown to readily emerge from depths to 2 cm in a field study (Grundy et al. 2003) or to 4 cm in a pot study (Benvenuti et al. 2001), so germination at depths greater than these could be fatal. However, redroot pigweed and common lambsquarters along with 18 other species were shown to undergo depth-induced dormancy, whereby approximately 85% of seed (90% of pigweed and lambsquarters) did not germinate (Benvenuti et al. 2001), a condition thought to be mediated by reduced oxygen levels with increased depth. This suggests that most seed at the 5- and 15-cm depths in our study would have been unlikely to undergo fatal germination.

Bags buried to either depth were temporarily exhumed during tillage operations in the spring and fall, thus potentially exposing seed near the surfaces of the bags to light. Light is a well-known stimulus to germination of Amaranthus and Chenopodium species and is particularly effective on seeds that have been sensitized by overwinter field burial or laboratory stratification (Bouwmeester and Karssen 1993; Gallagher and Cardina 1998a,b). Consequently, there was potential for fatal germination of some seed as a result of light exposure during bag transfer operations. However, the mechanisms of light induction can be complex because light is known to interact with many other factors such as temperature (both magnitude and diurnal amplitude), soil moisture, nitrates, and seed age for full expression to be achieved (Botto et al. 2000; Bouwmeester and Karssen 1993; Gallagher and Cardina 1998a,b; Henson 1970). In addition, reburial would have a potential counter effect of inducing dormancy by placement at depths with reduced oxygen as described above (Benvenuti et al. 2001). Thus, fatal germination from seed that had lost dormancy in these experiments is unknown but is a potential loss mechanism that may have been operative. Since the overall half-lives that we observed were similar to those reported by others, this mechanism was presumably not more operative in our experiments than in those reported by others. Since seeds in both systems were handled similarly, potential fatal germination probably does not explain the observed differences between systems.
Total soil microbial biomass, as measured by phospholipid fatty acid content, was highest in the organic systems at both locations, although the difference between the organic and conventional systems was only significant at the Rodale location (Table 3). Differences in total PLFA were driven primarily by higher levels of gram-negative PLFA in the organic system at both locations and higher levels of gram-positive PLFA in the organic system at Rodale. Higher PFLA levels of actinomycetes in the Rodale organic system and of eubacteria in the BARC organic system also contributed to total PLFA differences; whereas, eukaryote, fungi, and protozoa contributed negligibly to total PLFA levels.

Multivariate analysis of Hellinger transformed PLFA data (based on biomarker proportion) showed that the first canonical variate explained 95% of variation with a nonsignificant contribution by the second canonical variate (Figure 2). The BARC organic system data had the most positive values along the first canonical variate axis and the mean projection on this axis was significantly (P< 0.05) higher than all other systems according to MANOVA (1.77 for FSP organic vs. 0.002 for the BARC conventional system). The Rodale data were clustered to the negative side of the BARC data, and there was no significant difference between the Rodale organic and conventional system projected means (−0.87 and −1.15 for the Rodale organic and conventional systems, respectively). The gram-negative bacteria vector was associated with BARC organic system data at the positive end of the first canonical variate; whereas, actinomycetes and gram-positive bacteria vectors were associated with the conventional BARC and the Rodale data at the negative end of the axis.

Soil organic matter and microbial biomass and activity are often highly correlated in cropping systems (Buyer et al. 2010; Cookson et al. 2008; Kremer and Li 2003; Peacock et al. 2001). Since soil carbon was higher in the organic versus conventional systems at the initiation of these experiments (18.6 vs. 16.6 g kg−1 at BARC and 26.9 vs. 21.9 g kg−1 at Rodale, respectively), it is not surprising that total microbial PLFA biomass was higher in organic than conventional systems (Table 3). However, multivariate analysis of proportional PLFA data showed a divergence of organic systems at BARC and Rodale, with the BARC organic system most highly associated with the gram-negative bacteria vector (Figure 2).Buyer et al. (2010) have shown that gram-negative PLFAs tend to associate with systems with more utilizable carbon; whereas, gram-positive PFLAs are associated with more carbon-limited systems. Peacock et al. (2001) showed that a system with manure plus cover crops had greater microbial PLFA and a greater proportion of gram-negative bacteria than a system with only cover crops. In the systems reported here, both manure- and cover crop–based organic amendments were used in the BARC organic system, while the Rodale organic system was solely legume-based. Thus, the organic amendments used in the BARC organic system may have provided more available carbon for supporting a higher proportion of gram-negative bacteria than the Rodale organic system.
Correlations between Seed Persistence and Microbial PLFA.
There were very few significant correlations (P< 0.05) between PLFA biomarkers and seed persistence half-lives for Experiment 1 at both locations or for BARC Experiment 2 (data not shown). However, there were many significant negative correlations between PLFA biomarkers and seed persistence for Rodale Experiment 2 (Table 4). The highest correlations between biomarkers and persistence in Rodale Experiment 2 were found at the 5-cm depth for common lambsquarters (up to −0.64) and smooth pigweed (up to −0.55). Correlations were relatively similar for total PLFA, eubacteria, gram-positive and gram-negative bacteria, and actinomycetes for both species at this depth (Table 4). Correlations of these biomarkers with smooth pigweed persistence at 15 cm were lower than those at 5 cm, while there were no correlations for common lambsquarters at the 15-cm depth. The soil used for PFLA analysis, that came from a 0- to 15-cm sampling depth, was probably more representative of soil surrounding the seed at the 5-cm depth than at the 15-cm depth, thereby providing a possible explanation for higher correlations between microbial biomass and seed persistence at the 5-cm depth.

The absence of correlations between microbial PLFAs and seed persistence half-lives in Experiment 1 probably resulted from the relatively small range of differences between seed half-lives in organic and conventional systems with few significant differences at both locations (Table 1). In contrast, there was a greater range of differences between seed half-lives in organic and conventional systems in Experiment 2, but only at the Rodale location were these half-life differences correlated with microbial PLFA. At BARC, the opposite responses of smooth pigweed and common lambsquarters half-lives to system (Table 1) suggests that factors not associated with overall elevated levels of organic carbon and microbial biomass in organic systems were driving results. Given these unknown, but potentially complex set of factors driving results at this location, it is not surprising that there were no significant simple correlations between microbial PLFA and seed persistence at this location. The presence of correlations in the Rodale second experiment suggests that microbial activity could have been involved in seed mortality in this location-experiment. Higher microbial total PLFA (Table 3) and lower seed persistence of both species in organic vs. conventional systems in the Rodale second experiment (Table 1) provide plausibility that, in one of the four location-experiments reported here, the enhanced microbial hypothesis for weed seed mortality may have been operative.

The ambiguity of our results reflects a similar inconsistency in other research that has investigated relationships between soil organic matter, associated microbial populations, and weed seedbank persistence. Soil density of common lambsquarters seed was lower in a system relying on organic amendments than inorganic fertilizer (Gallandt et al. 1998); however, this was more likely due to lower weed biomass and seed production in this system than to higher seed mortality. Higher soil microbial biomass in California vegetable systems amended with cover crops and compost was associated with a lower weed seedbank and emergence in these systems (Fennimore and Jackson 2003); however, the lower seedbanks in these systems could have resulted from reduced seed production rather than increased seed mortality induced by higher microbial biomass. In contrast, experiments with seed buried in mesh bags across several midwestern states (Davis et al. 2005) or with seed incubated in soils from a range of cropping systems with varying levels of organic amendments (Davis et al. 2006) showed longer seed persistence in soils with higher organic carbon and organic amendments. However, later experiments with controlled levels of organic matter and nitrogen in a short-term controlled environment experiment, revealed no effect of these treatments on persistence of five of eight weed species, including redroot pigweed (Amaranthus retroflexus L.), but persistence of three species was shortened by these treatments through both fatal germination and seed mortality mechanisms (Davis 2007). Seed mortality in response to a range of organic-amended soils was negatively correlated to soil fungal 18S rRNA principal component values (Davis et al. 2006). Although the authors assigned “no direct biological meaning” to this metric, the general linkage of soil fungi with seed mortality is plausible since many experiments comparing seed persistence in fungicide-treated vs. untreated soil have shown that fungi can significantly contribute to seed mortality (Wagner and Mitschunas 2008).

At best, correlations between general metrics of microbial abundance or community structure and seed persistence can reveal potential associations, but they do not indicate causality. More importantly, they do not target the specific microbial biochemical activities that may be the primary mechanisms for seed mortality. Overall microbial biomass or community structure may not reflect the populations responsible for production of seed coat degrading enzymes, toxin production, or other activities detrimental to seed persistence. The seed coat is highly important for maintaining seed viability as shown by the rapid mortality of seeds with experimentally damaged seed coats and by the correlation of persistence with seed coat thickness (Davis et al. 2008). Sugars in seeds can form a viscous glassy state that physically stabilizes seed, suppresses deteriorating free-radical and enzymatic reactions, and provides for relatively high seed survivability. However, when this glass is weakened by increased water content and temperature (that could result from breaching the seed coat), a phase separation of sugars takes place, leading to initiation of rapid aging and seed mortality (Bernal-Lugo and Leopold 1998). Controlled aging treatments in the lab correlated to field persistence of seeds of 27 species suggesting that inherent biochemical resistance to moisture and temperature stress underlies aging and field persistence (Long et al. 2008). Thus, to understand the role of microbial agents in this complex process of seed protection against both aging and decaying influences, more precise and physiologically based research will be needed. Cropping system management may provide overall conditions that encourage enhanced microbial abundance and activity, but a more precise understanding of the mechanisms of seed mortality will be required in order to manage microbial populations for the targeted function of reducing weed seed viability.


This research was funded, in part, by a USDA-ARS Headquarters Research Associate Award. The authors are grateful for the technical oversight provided by Ruth Mangum and Stanley Tesch and to Jon Clark, Gloria Darlington, Jonathan Melzer, and Elizabeth Reed for the hours of patient work that this project required. We thank Bryan Vinyard, USDA-ARS Biometrics Consulting Service, for analysis of the seed persistence data.

Sources of Materials
1The Clorox Company, 1221 Broadway, Oakland, CA 94612.
2SAS software version 9.1.3, SAS Institute, Cary, NC 27513-2414.

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