BioBlitz

Microbes

 

Cayuga Nature Center   Smith Woods   Total species found
23,084   13,280   25,863

 

Humans rely on bacteria for everything from food production and digestion to the production of energy and pharmaceuticals. Microbes are the most diverse form of life on the Earth and they perform many functions that are important to the health of our biosphere. While some microbes are pathogens most are beneficial and without them plants and animals could not survive. Humans rely on microbes in many different ways. Digestion of plant material is largely dependent on the activities of microbes in the large intestine. These microbes help provide humans and other animals with vitamins and nutrients that are important for health and well-being. Humans also interact with microbes in agriculture. Plant microbiomes and plant pathogens influence plant health, and soil microbes provide the foundation for soil fertility. In the food industry microbes are used to make and preserve foods. Additionally, microbes are essential components for treating drinking and wastewater. Microbes are also used in mining and industrial production, as well as in the production of biofuels such as ethanol and methane. In biotechnology microbes are used to produce a variety of pharmaceuticals.

Over 90% of the species found were not named or well known to science! 

Methods

Identification method follows a strict set of steps: 

  • Extract DNA
  • Amplify 16S rRNA genes using Polymerase Chain Reaction
  • Barcode DNA from each sample
  • Sequence the amplified genes using Illumina MiSeq
  • 161 samples with good results
  • 10.7M total sequences (average of ~66459 sequences/sample)
  • 16S rRNA gene sequence allows for species level identification.

Findings

In general tree and plant microbiomes were the most diverse, but the number of species found differed within sample types. Some samples from the skin of critters had a large number of species (Toad and Salamander), while some had few (Bullfrog Tadpole and Bullfrog). The feather sample had a surprising number of bacterial species. This may indicate that feather collect bacteria from a variety of places where a bird visits. In contrast to the diverse bacteria found in water, leaf, and soil samples, the animal microbiomes samples tended to contain a highly distinct set of bacteria. Thisdemonstrates that each animal is selecting for certain types of microbes, in essence creating its own curated microbiome!  Plant leaves contained the greatest number of bacterial species! Team Microbe used DNA sequencing to identify species of Bacteria at the Cayuga Nature Center. A microbiome is the collection of microbes associated with particular habitat or organism. The team sampled the microbiomes of soils, water, plants, animals, and fungi. Water and soil samples contained the most bacterial species but every plant and animal was home to a diverse collection of bacterial species.

It was expected that soils of the area would be the most diverse habitat for bacteria. While soils were indeed highly diverse, the creek site was actually found to have the highest diversity. Sampling and analysis showed that the creek was collecting microbes from the entire watershed. Only a small number of bacterial species found in the creek were unique to the creek itself, and most of the bacteria found in it were also found in soils, plants, and animals. This might be a different story if the stream were lower flow, but the sampling did take place the day after rain. Around the Nature Center, streams, ponds and the slippery stuff that forms on rocks called ‘biofilms’ were sampled. Biofilms are where microbes cement themselves together to create a thriving community, much like humans might on Mars. Cyanobacteria were much more abundant in the biofilms than either pond or stream water. Microbes are the most diverse form of life on the Earth and they perform many functions that are important to the health of our biosphere. While some microbes are pathogens most are beneficial and without them plants and animals could not survive.

25863 Species were found! 

Participants

Team Microbe had 15 participants including four faculty and 11 grad students. The participants came from the Section of Soil and Crop Sciences, the Section of Plant Pathology and Plant Microbe Biology and the Department of Microbiology at Cornell. Daniel H. Buckley led the soil sampling, Esther Angert (Microbiology) led the animal sampling, Tory Hendry (Microbiology) led the plant sampling, and Kalia Bistolis (Microbiology) led the aquatic sampling.