Monoculture and Soil Microbes

Pseudostellaria heterophylla
Pseudostellaria heterophylla and its medicinal tubors

As the human population continues to grow, agricultural systems face more and more pressure to increase crop production. This demand has resulted in the domination of several staple crops, such as wheat, corn, and soy, in human diet and thus in the fields of many industrial farms. This transition has led many farmers to plant and replant large areas of land with a single crop, a practice known as monoculture. However, while monoculture may initial yield impressive results, over time, the health of the crops decline and production is reduced (Biodiversity and Agriculture, 2016). Much effort has been put into understanding this process to optimize the health of the crops to ensure the future of producing enough food to meet the demands of the human population.

A new study suggests that the practice of monoculture shifts the structure of the soil microbiome, which in turn negatively impacts the health of the crop (McNear, 2013). The microbial life inhabiting the soil immediately surrounding the roots of a plant, an area known as the rhizosphere, is known to play important roles in the health of the plant from nutrient acquisition to defense against pathogens (Zhao, 2016). Likewise, roots often secrete compounds that attract or repel microbes, thus shaping the population of microbes that they associate with. In this study, the authors hypothesize that the successive replanting of the same crop alters the compounds that roots secrete, which consequently disrupts the soil microbiome and the function that it serves to the crop. They used the replanting of Pseudostellaria heterophylla, a crop commonly used in Chinese medicine, to investigate the effects of monoculture on soil microbes. P. heterophylla grows best in a specific part of southeast China, but intensive cultivation in the same area has started to result in declining health and production of the crop. Attempts to grow the crop in less desirable areas have had little success, so there is considerable need to understand the relationship between monoculture and crop health. The authors looked both at the overall impact on the abundance and diversity of soil microbes, as well as the specific impact on a few species with known beneficial or pathogenic relationships to the crop.

The authors analyzed the soil in fields that had not been planted, fields that had been planted with P. heterophylla for the first time, and fields that had been replanted with P. heterophylla. They found that the replanted soil had fewer species of microbes than the unplanted or newly planted soil, and that the replanted soil had fewer species in common with the unplanted soil than the newly planted soil had. In other words, replanting P. heterophylla reduced the diversity of microbes and altered which species were present. The authors looked more closely at the second finding and found that replanted soil contained less beneficial bacteria, such as those that aid in element cycling and nutrient absorption, and more harmful bacteria, such as denitrifying bacteria and pathogens, than unplanted or newly planted soil. The authors also identified specific species of microbes with known functions and analyzed their response to replanting. Pathogenic fungal and bacterial species increased in the replanted soil from the unplanted and newly planted soil, and beneficial bacterial species decreased. The authors provide ample evidence to suggest that the detrimental effects of monoculture result from the disruption of the soil microbe population after successive replanting of the same crop. This study introduces many more questions around how to sustainably maintain healthy crops. Is there a way to restore the population of beneficial microbes to maintain the health of the plants? We are only beginning to learn about the abundance of life that is too small for us to see, and much more research is required before we will be able to employ them to our benefit. Even so, the soil microbiome offers an exciting new avenue for research into how to optimize the health of crops so that they can be grown sustainably in the numbers required to meet the needs of our growing population.


“Biodiversity and Agriculture.” The Center for Health and the Global Environment. N.p., n.d. Web. 16 June 2016.

McNear Jr, D. H. “The rhizosphere-roots, soil and everything in between.”Nature Education Knowledge 4.3 (2013): 1.

Zhao, Yong-Po, et al. “Insight into structure dynamics of soil microbiota mediated by the richness of replanted Pseudostellaria heterophylla.”Scientific reports 6 (2016).


Using the Baleen Whale to Explore the Gut Microbiome

Baleen Whale
A humpback whale is a species of baleen whale

With the growing evidence of the presence and importance of microorganisms in our bodies, there has been more interest in exploring what factors shape these communities. Previous studies have identified diet as a major determinant of the intestinal microbiome (Ley, R. E. et al. 2008). Many animals that eat similar diets have host similar species of microbes. Some anomalies, such as the Giant Panda, suggest that there are other factors shaping the microbiome (Xue, Z. et al. 2015). The Giant Panda feeds primarily on bamboo and its closest relatives are omnivorous bears. Despite the discrepancies in diet, the panda’s microbiome is much more similar to that of its omnivorous relatives than other herbivores, which suggests that there is more to the development of the microbiome than diet. Are there aspects of the microbiome that are predetermined at birth that cannot be changed by diet? One possible factor is the structure of the stomach itself. Many herbivores have multichambered stomachs that house bacteria specific for fermenting carbohydrates from the plants they eat, but the giant panda still has a relatively simple stomach like its omnivorous ancestors. Could it be that even though its diet has changed, the morphology of its digestive system simply isn’t a suitable home for the microbes that normally are present in herbivores?

A new study delves into this issue by focusing on the microbiome of baleen whales, another animal whose diet differs dramatically from its close relatives (Sanders, J. G. et al. 2015). Although whales are carnivores, feeding on other animals like fish and krill, their closest relatives are terrestrial herbivores like hippopotamus, deer, and giraffe. Although the whale diets have changed drastically since they diverged from their terrestrial ancestors, their digestive systems may not have. Like their herbivorous relatives, whales possess a multichambered stomach that may be used for fermenting carbohydrates (Gatesy, J. et al. 2013). The authors hypothesize that this structural development could play a role in shaping the microbiome in addition to diet.

To investigate this idea, the authors sequenced the microbial DNA from fecal samples to determine which microbes were present in the intestines of different organisms. They also analyzed enzyme expression and the activity of microbial proteins to determine what function these microbes had. At first glance, their results hardly seem to clarify the issue; on the whole, the whale microbiome seems to be distinct from both carnivores and herbivores. Furthermore, when separating microbial genes by function, such as energy or lipid metabolism, they found similarities to both terrestrial herbivores and carnivores. However, by looking at these results in light of the idea that a multichambered stomach fosters carbohydrate fermentation, a pattern appears to emerge.

The authors found that the whale microbiome is similar to that of terrestrial herbivores for genes related to the metabolism of carbon and specifically fermentation. Pyruvate, for example, is a major intermediate molecule in fermentation, and both herbivore and whale microbiomes contain genes related to metabolizing pyruvate. They also have genes for enzymes involved with producing short chain fatty acids, which is an end product of microbial fermentation. These and other similarities suggest that the fermentation of carbohydrates during digestion is one factor shaping the microbiome.

Whales differed from terrestrial herbivores in the enzymes their microbiomes expressed for carbohydrate metabolism. The source of carbohydrates differs between whales and terrestrial herbivores, with whales primarily being chitin from the exoskeletons of arthropods and terrestrial herbivores primarily being cellulose from plants, so different enzymes are needed to specifically break down these molecules. Thus, diet clearly influences the microbiome, but within the context of the overall digestive process, since both groups of animals housed microbes for fermentation.

Indeed, when the whale microbiome was compared to that of other animals that eat chitin but that don’t have a multichambered stomach that would allow fermentation, there were important differences. Armadillos and echidnas both eat arthropods with chitinous exoskeletons, and they have relatively simple stomachs. Unlike whales, their microbiomes did not express enzymes related to the digestion of chitin. Although whales, armadillos, and echidnas all consume chitin, enzymes to digest it are only present in whales, suggesting that the physical structure of the digestive tract plays an important role in shaping the microbiome.

Clearly there is more to the intestinal microbiome than diet. This study proposes that physiology, as determined by the evolutionary development of an animal, also plays a role. This idea opens the door for more exploration into how the way bodies are built influences what microscopic organisms can inhabit them as well as what other as of yet unknown of factors are out there.


Gatesy, J. et al. A phylogenetic blueprint for a modern whale. Mol. Phylogenet. Evol. 66,479–506 (2013).

Ley, R. E. et al. Evolution of mammals and their gut microbes. Science 320, 1647–1651(2008).

Sanders, J. G. et al. Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. Nat. Commun. 6:8285 doi: 10.1038/ncomms9285 (2015).

Xue, Z. et al. The bamboo-eating giant panda harbors a carnivore-like gut microbiota, with excessive seasonal variations. MBio. 6, e00022–15 (2015).


New Study Analyzes Pollution in Northern China Using Lichens

We are constantly hearing about the latest technological advances, but sometimes the most effective tools can be found in nature. For example, our complex man-made air pollution monitoring systems are usually limited to detecting only a few pollutants (Liu et. al 2016). By utilizing lichens, on the other hand, we can get measurements on a wide range of elements. Since they are widespread, we can also get a sense of how pollutants travel and spread from their source without needing to install machinery at every site.

Understanding why analyzing lichens can be so representative of the pollutants in the environment requires an understanding of lichen biology. Although lichens are often thought of as their own organism, they are actually composed of two organisms, a fungus and either cyanobacteria or algae. In these symbiotic relationships, each organism benefits by the presence of the other. Both cyanobacteria and algae are photosynthesizing organisms, so they produce organic molecules that the fungus can use as fuel. The fungus provides structural support that anchors and protects its photosynthesizing partner. The resulting life form does not require the roots, vascular system, or protective cuticle that are characteristic of many photosynthesizing plants. The lack of these structures allows lichens to absorb water and nutrients that are deposited from the atmosphere on their bodies. Thus, the composition of elements in the lichens is reflective of the composition of elements in the air, so scientists can infer the level of certain elements in the atmosphere to monitor air quality based on the levels of these elements in lichens (Bari et al. 2001).

Lichens have been used to monitor pollution for about two decades in a variety of environments such as the Arctic, China, Portugal, France, North Dakota, and Italy (Liu et al. 2016). Many of these studies have been geared toward understanding the contributions of anthropogenic activities on air quality. A study in the southwest of France focused on how atmospheric factors have changed over time with the changes in human activity by utilizing lichens preserved from the early twentieth century (Agnan, Séjalon-Delmas, & Probst, 2013). A new study published in Nature focused on the North China Plain (Liu et al. 2016), where recent urbanization and industrialization has stimulated concern about environmental pollution. The study used lichens to investigate the level of contamination of both soil and air, as well as the extent to which pollutants are localized or able to travel.

The study focused on the Taihang Mountains of the Hebei Province. Industry in the Hebei Province produces in the highest levels of crude steel output in China (Tian et al. 2015). Intensive agricultural efforts and heavy automotive traffic also contribute to the high rates of emissions in the area. This pollution has already resulted in aerosol smog, particulate storms, and acid rain in Northern China, leading the authors to investigate the prevalence and persistence of the pollutants in the surrounding ecosystem.

The authors measured the lichen concentrations of thirty trace elements and used a value called the enrichment each to characterize each as likely sourced from the soil or likely sourced from the atmosphere. The enrichment factor represents the concentration of the element in the lichen related to its concentration in the soil. Therefore, elements that were considerably more concentrated in the lichen than in the soil, an enrichment factor greater than 5, were considered to have an atmospheric source. In addition to determining the source of the elements, the authors sought to map their concentrations over the whole sampling area and investigate any patterns. Indeed, this analysis revealed an increase in the concentration of many crustal and atmospheric elements near mining activities. They also found evidence for the transportation of some crustal elements northward by windblown soil particulates and some atmospheric elements by southeast and east winds. Regardless of the source, all of the elements they measured were more concentrated in the lichens than most of the previously measured values from other sources, which suggests that the pollution of industrial activities in Northern China is having a significant presence in the surrounding ecosystems.

The authors emphasize the importance of addressing the prevalence of pollution that their lichen analysis has revealed. Lichens have proven to be an effective tool at monitoring the effects of industrial emissions on the surrounding environment, but even more work will be needed to address the issues that these investigations reveal.


Agnan, Y., Séjalon-Delmas, N., & Probst, A. (2013). Comparing early twentieth century and present-day atmospheric pollution in SW France: a story of lichens. Environmental pollution172, 139-148.

Bari, A., Rosso, A., Minciardi, M. R., Troiani, F., & Piervittori, R. (2001). Analysis of heavy metals in atmospheric particulates in relation to their bioaccumulation in explanted Pseudevernia furfuracea thalli. Environmental Monitoring and Assessment69(3), 205-220.

Liu, H. J., Zhao, L. C., Fang, S. B., Liu, S. W., Hu, J. S., Wang, L., … & Wu, Q. F. (2016). Use of the lichen Xanthoria mandschurica in monitoring atmospheric elemental deposition in the Taihang Mountains, Hebei, China.Scientific Reports6.

Tian, H. Z., Zhu, C. Y., Gao, J. J., Cheng, K., Hao, J. M., Wang, K., … & Zhou, J. R. (2015). Quantitative assessment of atmospheric emissions of toxic heavy metals from anthropogenic sources in China: historical trend, spatial distribution, uncertainties, and control policies. Atmospheric Chemistry and Physics15(17), 10127-10147.