Background, This Week In The Lab

Niche Theory In Everyday Life

SYDNEY, AUS: In the day to day here, as I commute to work, take the bus around town, and observe, I’m frequently overwhelmed by daily demonstrations of niche theory and convergent evolution in the world around me. The terrestrial flora in Sydney is of an entirely different lineage, primarily of the Myrtoideaen tribe Eucalypteae, than what I know from the Pacific Northwest. Though Eucalypts have long been present on Earth, their radiation in Australia is apparently relatively recent. Eucalypts now make up ¾ of the vegetation on this island continent, and fill nearly every ecological function that I, as a North American, attribute to other trees. For instance, coastal swamplands similar to the cypress swamps of Louisiana and Texas are here inhabited by swamp gum trees, other Eucalyptus spp., and their Myrtoideaen cousins, the paperbark trees. Savanna and temperate grassland habitats that in the US would have scattered oaks, cottonwoods, or willows, are here are inhabited by bimble box and coolibah eucalyptus trees. The Sydney red gum is one of several Eucalypts that plays the role of North American fruit trees, providing food for fruigivores. On my commute home at night, I often get to watch enormous ‘flying foxes’, or Ku-ring-gai bats (Pteropus poliocephalus), indulging in the tree’s nectar.

This, of course, is entirely tangential from my work on man-made alterations to urban shorelines in Sydney Harbour. While I know I should be entirely focused on the project that brought me here, the natural history nerd within has a hard time ignoring what Darwin and many others since found astonishing upon first traveling to the opposite hemisphere: That a similar set of ecological professions (niches) exist everywhere, and who fills them (which species) is heavily influenced by chance.

Post about ancient Eucalyptus from Eliza’s Instagram

Eliza’s instagram

Standard
This Week In The Lab

Next Generation Sequencing – Life Forms of Sydney Harbor

Leonard Nimoy as Spock from Star Trek: The Original Series.

In the original Star Trek, Lieutenant Spock, upon beaming down to a new planet from the Starship Enterprise, would immediately pull out a Tricorder and begin scanning the environment for life forms. Results were instantaneous, providing a comprehensive view of the surrounding ecosystem within seconds.

Though we have yet to fully see such a novel invention on Earth, I’m overwhelmed today by how close we actually are to inventing the Tricoder in real life. I spent the day in lab at the Sydney Institute of Marine Science, extracting DNA from marine sediments and their invertebrate inhabitants. Thanks to support from the IGERT Program on Ocean Change at UW and from the Applied Marine and Estuarine Ecology Lab at UNSW, the genetic material I extracted will be sequenced and matched to a database of known organism sequences, in a process called DNA barcoding.

Eliza looking very serious in her white lab coat

Like DNA extractions of the old school variety, the endeavor required donning a white lab coat, goggles, and gloves, and making sure not to sneeze or shed excessively. Unlike genetic adventures past, the materials needed for the extractions were available in a self-contained kit shipped par avion from Texas — no gels or interpretation of specific sequences was needed, and the entire process for many 10s of samples took only a single work day (20 years ago, comparable work might have been the focus of an entire PhD).

Vials and pipetting tools for the final stage of DNA extractions

I hope results from the day’s genetic escapades will yield helpful information about both the microbial and invertebrate community on manmade and natural shorelines in urban settings, such as Sydney. And I’m thrilled to report there is a chance that by the end of my lifetime, I could be scanning Earth’s ecosystems, Tricoder in hand, with my best interpretation of a female embodiment of Lieutenant Spock.

Tricorder from Star Trek: The Next Generation.

Standard
This Week In The Lab

Hello again from down under

Hello again from down under! Henna Wilckens (intern) and I are deep into processing the sediment samples we collected last month from the bottom of Sydney Harbour. From our temporary work post at the University of New South Wales, we aim to sort through each of the millions of tiny sediment grains in our frozen samples to extract anything that once wriggled, crawled, filtered, or respired. The identity and number of creepy crawly critters in our samples will help us discern whether marine communities adjacent to man-made seawalls and pilings differ from those adjacent to natural rocky shorelines. All of this is part of a project I’m doing as an NSF EAPSI fellow with my Australian host, Dr. Emma Johnston, and post-doctoral researchers in her lab (link to earlier post).

Surprising as it may be, we’ve thus far encountered a number of striking and beautiful organisms within the urban muck.

A carnivorous polychaete worm from Syndey Harbor

Snail from Sydney Harbor

A snail cacophony from Syndey Harbor

Ostracods (tiny shelled crustaceans) from Sydney Harbor

Foraminifera from Sydney Harbor

Single foraminifera

Standard